Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics
How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. pepti...
Saved in:
| Published in | Biochimica et biophysica acta Vol. 1864; no. 8; pp. 883 - 895 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Netherlands
Elsevier B.V
01.08.2016
Elsevier |
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic peaks and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics— a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
•Many methods to quantify and compare protein abundances in bottom-up proteomics•Two complementary approaches: identification-based and XIC-based•Identification-based approach is better suited for detection of large abundance variations.•XIC-based approach is more sensitive.•No gold standard method at present |
|---|---|
| AbstractList | How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic peaks and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic pealcs and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics- a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. (C) 2016 Elsevier B.V. All rights reserved. How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic peaks and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics— a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. •Many methods to quantify and compare protein abundances in bottom-up proteomics•Two complementary approaches: identification-based and XIC-based•Identification-based approach is better suited for detection of large abundance variations.•XIC-based approach is more sensitive.•No gold standard method at present |
| Author | Zivy, Michel Blein-Nicolas, Mélisande |
| Author_xml | – sequence: 1 givenname: Mélisande surname: Blein-Nicolas fullname: Blein-Nicolas, Mélisande – sequence: 2 givenname: Michel surname: Zivy fullname: Zivy, Michel email: zivy@moulon.inra.fr |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26947242$$D View this record in MEDLINE/PubMed https://hal.science/hal-01532597$$DView record in HAL |
| BookMark | eNqFkctu1TAQhi1URC_wBghlCYsE3y8bpKoCinQkNmVtjR1H9VESp3FSdN6-DildwsKyZ_z9M6P5L9HZmMaA0HuCG4KJ_HxsnIMJpoaWqMG0wcS8QhdEK10TLvhZeQuFayOZOUeXOR8xplgp8QadU2m4opxeIH93n9YMY1ttp3SofsMpV0uqHlYYl9id_nz4NEwwh2qa0xLiWIFbxxZGH3JVoh5c6OtuDqFyaVnSUK_TjqYh-vwWve6gz-Hd832Ffn37endzWx9-fv9xc32oPTdiqblQhjggHAthJCeMOc2VDwpYR53uIGhGMUAnu050QmpiHONSeaCagaTsCn3a695Db6c5DjCfbIJob68PdsthIhgVRj2Swn7c2TLmwxryYoeYfeh7GENZiCUaa8kwLYr_ospIqbfKBeU76ueU8xy6lzEItptr9mh31-zmmsW0zGSK7MNzh9UNoX0R_bWpAF92IJT1PcYw2-xjKOtv4xz8YtsU_93hCYUaquI |
| CitedBy_id | crossref_primary_10_1002_jex2_103 crossref_primary_10_3390_ijms21041524 crossref_primary_10_3390_ijms18122677 crossref_primary_10_1002_elps_201700220 crossref_primary_10_1016_j_pbi_2021_102061 crossref_primary_10_1021_acs_jproteome_7b00163 crossref_primary_10_1021_acs_jproteome_2c00803 crossref_primary_10_1016_j_jprot_2017_04_004 crossref_primary_10_1007_s11064_018_2636_2 crossref_primary_10_1039_D0MO00045K crossref_primary_10_1016_j_npep_2018_11_002 crossref_primary_10_1016_j_ecoenv_2019_109421 crossref_primary_10_1021_acs_jproteome_6b00066 crossref_primary_10_1021_acs_jproteome_8b00769 crossref_primary_10_1021_acs_jproteome_3c00714 crossref_primary_10_1038_s41598_020_65087_w crossref_primary_10_1128_msystems_00026_22 crossref_primary_10_1016_j_csbj_2023_07_027 crossref_primary_10_1371_journal_pone_0276401 crossref_primary_10_1016_j_jprot_2018_10_003 crossref_primary_10_1074_mcp_TIR118_001086 crossref_primary_10_1073_pnas_2219801120 crossref_primary_10_1002_bmc_4523 crossref_primary_10_1021_acs_jproteome_1c00143 crossref_primary_10_1039_C6MB00278A crossref_primary_10_3390_proteomes10010002 crossref_primary_10_15252_embr_201643846 crossref_primary_10_1021_acs_analchem_9b04375 crossref_primary_10_1186_s40824_022_00284_4 crossref_primary_10_1002_mas_21837 crossref_primary_10_1038_s41597_020_00744_3 crossref_primary_10_1371_journal_pone_0238037 crossref_primary_10_1021_jacs_1c03321 crossref_primary_10_1146_annurev_anchem_061516_045357 crossref_primary_10_1537_asj_200213 crossref_primary_10_3389_fimmu_2019_02067 crossref_primary_10_1016_j_aca_2017_01_057 crossref_primary_10_1371_journal_pgen_1010618 crossref_primary_10_1021_acs_jproteome_7b00786 crossref_primary_10_1016_j_foodchem_2024_139871 crossref_primary_10_1186_s12014_017_9171_z crossref_primary_10_1161_JAHA_121_024769 crossref_primary_10_3390_proteomes6020027 crossref_primary_10_1016_j_jprot_2020_103985 crossref_primary_10_1016_j_jprot_2020_103884 crossref_primary_10_1016_j_mcpro_2023_100518 crossref_primary_10_3389_fmicb_2021_616050 |
| Cites_doi | 10.1021/pr500741y 10.1002/pmic.201000521 10.1021/acs.jproteome.5b00183 10.1074/mcp.M110.007203 10.1093/biomet/5.3.351 10.1002/pmic.201100120 10.2202/1544-6115.1027 10.1142/S0219720008003321 10.1016/j.jasms.2007.11.013 10.1002/pmic.200900437 10.1186/1471-2105-13-S16-S4 10.1074/mcp.M800203-MCP200 10.1021/pr900252n 10.1007/978-1-61779-885-6_20 10.1101/gr.7.10.986 10.1038/nbt.1511 10.1002/pmic.201000553 10.1002/pmic.201000800 10.1093/bioinformatics/btu200 10.1186/1471-2105-5-203 10.1186/1471-2105-9-529 10.1093/bioinformatics/btp677 10.1186/gb-2010-11-10-r106 10.1038/nature01111 10.1002/(SICI)1097-0231(19990730)13:14<1427::AID-RCM662>3.0.CO;2-5 10.1021/pr9000866 10.1186/1471-2105-13-S16-S6 10.1038/nature10098 10.1093/bioinformatics/btg264 10.4310/SII.2012.v5.n1.a7 10.1016/j.jprot.2015.07.012 10.1021/pr401096z 10.1038/nbt.1661 10.1186/s13059-014-0550-8 10.1074/mcp.M500230-MCP200 10.1016/j.jprot.2010.08.009 10.1214/aoms/1177730491 10.1016/j.febslet.2004.07.055 10.1074/mcp.M113.031591 10.1586/epr.09.69 10.1586/epr.09.107 10.1021/pr501045t 10.1002/pmic.200700426 10.1074/jbc.M400103200 10.1074/mcp.M500061-MCP200 10.1021/pr400438q 10.1186/1471-2105-13-308 10.1074/mcp.O115.048181 10.1128/MCB.19.11.7357 10.1002/pmic.201100660 10.1021/pr401206m 10.1101/gr.473902 10.1021/pr070271+ 10.1038/nbt1270 10.1021/pr100527g 10.1093/bioinformatics/btu341 10.1038/85686 10.1021/ac0498563 10.1074/mcp.M700240-MCP200 10.1093/bioinformatics/bth092 10.1089/cmb.2009.0267 10.1002/pmic.200900328 10.1021/pr200219x 10.1111/j.1420-9101.2009.01888.x 10.1021/pr070441i 10.1002/pmic.201000650 10.1093/clinchem/47.8.1350 10.1002/pmic.201400323 10.1016/j.jprot.2015.07.036 10.1021/pr034038x 10.1021/pr050109b 10.1074/mcp.M112.025445 10.1021/cr3003533 10.1021/ac9004887 10.1074/mcp.M110.002774 10.1021/pr400100k 10.1021/ac9023999 10.1002/pmic.201300135 10.1093/bioinformatics/btq171 10.1021/pr900610q 10.1074/mcp.R112.025163 10.1021/pr060161n 10.1128/MCB.24.16.7249-7259.2004 10.1021/pr201052x 10.1039/C3AN01738A 10.1186/1471-2105-9-316 10.1109/tcbb.2007.1078 10.1038/nbt.1592 10.1093/bioinformatics/btp362 10.1074/mcp.M600222-MCP200 10.1093/bioinformatics/bts449 10.1093/bioinformatics/btn217 10.1073/pnas.091062498 10.1039/c2an35173k 10.1021/pr501138h 10.1021/pr025517j 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10.1093/bioinformatics/btp700 10.1002/pmic.201200269 10.1021/pr0600273 10.1080/01621459.1952.10483441 10.1021/pr015518w 10.1016/j.jprot.2012.06.020 10.1021/pr401017h 10.1016/j.jprot.2010.05.011 |
| ContentType | Journal Article |
| Copyright | 2016 Elsevier B.V. Copyright © 2016 Elsevier B.V. All rights reserved. Distributed under a Creative Commons Attribution 4.0 International License |
| Copyright_xml | – notice: 2016 Elsevier B.V. – notice: Copyright © 2016 Elsevier B.V. All rights reserved. – notice: Distributed under a Creative Commons Attribution 4.0 International License |
| DBID | CGR CUY CVF ECM EIF NPM AAYXX CITATION 7X8 7QO 8FD FR3 P64 1XC |
| DOI | 10.1016/j.bbapap.2016.02.019 |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed CrossRef MEDLINE - Academic Biotechnology Research Abstracts Technology Research Database Engineering Research Database Biotechnology and BioEngineering Abstracts Hyper Article en Ligne (HAL) |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) CrossRef MEDLINE - Academic Engineering Research Database Biotechnology Research Abstracts Technology Research Database Biotechnology and BioEngineering Abstracts |
| DatabaseTitleList | MEDLINE MEDLINE - Academic Engineering Research Database |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Anatomy & Physiology Statistics Chemistry |
| EISSN | 1878-1454 |
| EndPage | 895 |
| ExternalDocumentID | oai_HAL_hal_01532597v1 10_1016_j_bbapap_2016_02_019 26947242 S1570963916300322 |
| Genre | Journal Article Review |
| GroupedDBID | --- --K --M .~1 0R~ 1B1 1RT 1~. 1~5 23N 4.4 457 4G. 53G 5GY 5RE 5VS 7-5 71M 8P~ AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AARLI AAXUO ABFNM ABGSF ABMAC ABUDA ABXDB ABYKQ ACDAQ ACIUM ACNNM ACRLP ADBBV ADECG ADEZE ADMUD ADUVX AEBSH AEHWI AEKER AFKWA AFTJW AFXIZ AFZHZ AGHFR AGRDE AGUBO AGYEJ AIEXJ AIKHN AITUG AJBFU AJOXV AJSZI ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ AXJTR BKOJK BLXMC CS3 DOVZS EBS EFJIC EFLBG EJD EO8 EO9 EP2 EP3 FDB FEDTE FIRID FLBIZ FNPLU FYGXN G-Q GBLVA HVGLF HZ~ IHE J1W KOM M41 MO0 N9A O-L O9- OAUVE OZT P-8 P-9 PC. Q38 RNS ROL RPZ SCB SCU SDF SDG SDP SES SEW SPC SPCBC SSK SSU SSZ T5K ~G- -~X .55 .GJ 3O- AAQXK AAYJJ ABEFU ABJNI AFFNX AHHHB AI. AKRWK ASPBG AVWKF AZFZN CGR CUY CVF ECM EIF F5P FGOYB G-2 HLW H~9 K-O LX3 MVM NPM OHT R2- RIG SBG TWZ UHS VH1 WH7 WUQ X7M XJT Y6R YYP ZE2 ZGI ~KM AAXKI AAYXX AFJKZ CITATION 7X8 7QO 8FD FR3 P64 1XC |
| ID | FETCH-LOGICAL-c495t-45791ba14055964133b847ce7a3f2b8fae8320aaf6ff5f56819b3467ca283a623 |
| IEDL.DBID | .~1 |
| ISSN | 1570-9639 0006-3002 |
| IngestDate | Fri Sep 06 12:42:09 EDT 2024 Fri Aug 16 10:06:13 EDT 2024 Fri Aug 16 22:50:18 EDT 2024 Thu Sep 26 18:30:02 EDT 2024 Tue Aug 27 13:56:32 EDT 2024 Fri Feb 23 02:13:13 EST 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 8 |
| Keywords | SC XIC FDR Data processing LC–MS/MS Mass spectrometry Statistics Peptide TOTAL ION CURRENT TANDEM MASS-SPECTROMETRY LC-MS PROTEOMICS SPECTRAL COUNT DATA LIQUID-CHROMATOGRAPHY ABSOLUTE PROTEIN FREE SHOTGUN PROTEOMICS DIFFERENTIALLY EXPRESSED GENES FREE QUANTITATIVE PROTEOMICS PEPTIDE QUANTIFICATION |
| Language | English |
| License | Copyright © 2016 Elsevier B.V. All rights reserved. Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c495t-45791ba14055964133b847ce7a3f2b8fae8320aaf6ff5f56819b3467ca283a623 |
| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-3 content type line 23 ObjectType-Review-1 ObjectType-Article-1 ObjectType-Feature-2 |
| ORCID | 0000-0001-6026-4989 |
| PMID | 26947242 |
| PQID | 1796685325 |
| PQPubID | 23479 |
| PageCount | 13 |
| ParticipantIDs | hal_primary_oai_HAL_hal_01532597v1 proquest_miscellaneous_1808630215 proquest_miscellaneous_1796685325 crossref_primary_10_1016_j_bbapap_2016_02_019 pubmed_primary_26947242 elsevier_sciencedirect_doi_10_1016_j_bbapap_2016_02_019 |
| PublicationCentury | 2000 |
| PublicationDate | 2016-08-01 |
| PublicationDateYYYYMMDD | 2016-08-01 |
| PublicationDate_xml | – month: 08 year: 2016 text: 2016-08-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | Netherlands |
| PublicationPlace_xml | – name: Netherlands |
| PublicationTitle | Biochimica et biophysica acta |
| PublicationTitleAlternate | Biochim Biophys Acta |
| PublicationYear | 2016 |
| Publisher | Elsevier B.V Elsevier |
| Publisher_xml | – name: Elsevier B.V – name: Elsevier |
| References | Mann, Whitney (bb0285) 1947; 18 Bilbao, Varesio, Luban, Strambio-De-Castillia, Hopfgartner, Müller, Lisacek (bb0020) 2015; 15 Shinoda, Tomita, Ishihama (bb0125) 2010; 26 Audic, Claverie (bb0305) 1997; 7 Ying Zhang (bb0160) 2009; 81 Zhang, VerBerkmoes, Langston, Uberbacher, Hettich, Samatova (bb0280) 2006; 5 MacLean (bb0085) 2010; 23 Bourmaud, Gallien, Domon (bb0015) 2014 Hawkridge (bb0025) 2014 Pavelka, Fournier, Swanson, Pelizzola, Ricciardi-Castagnoli, Florens, Washburn (bb0295) 2008; 7 Peng, Kim, Cheng, Duong, Gygi, Sheng (bb0180) 2004; 279 Colaert, Gevaert, Martens (bb0240) 2011; 10 Tusher, Tibshirani, Chu (bb0335) 2001; 98 Powell, Weaver, Jennings, McAfee, He, Weil, Link (bb0175) 2004; 24 Pang, Ginanni, Dongre, Hefta, Opiteck (bb0150) 2002; 1 Perkins, Pappin, Creasy, Cottrell (bb0045) 1999; 20 Rardin, Schilling, Cheng, MacLean, Sorenson, Sahu, MacCoss, Vitek, Gibson (bb0540) 2015; 14 Daly, Anderson, Panisko, Purvine, Fang, Monroe, Baker (bb0095) 2008; 7 Cox, Mann (bb0080) 2008; 26 Lundgren, Hwang, Wu, Han (bb0215) 2010; 7 Chelius, Bondarenko (bb0070) 2002; 1 Valot, Langella, Nano, Zivy (bb0075) 2011; 11 Webb-Robertson, Wiberg, Matzke, Brown, Wang, McDermott, Smith, Rodland, Metz, Pounds, Waters (bb0390) 2015; 14 Silva, Gorenstein, Li, Vissers, Geromanos (bb0405) 2006; 5 Langley, Mayr (bb0340) 2015; 129 Freund, Prenni (bb0535) 2013; 12 Ishihama, Oda, Tabata, Sato, Nagasu, Rappsilber, Mann (bb0120) 2005; 4 Breitling, Armengaud, Amtmann, Herzyk (bb0450) 2004; 573 Karpievitch, Stanley, Taverner, Huang, Adkins, Ansong, Heffron, Metz, Qian, Yoon, Smith, Dabney (bb0385) 2009; 25 Kannaste, Suomi, Salmi, Uusipaikka, Nevalainen, Corthals (bb0165) 2014; 13 Pham, Piersma, Warmoes, Jimenez (bb0265) 2010; 26 Benjamini, Hochberg (bb0345) 1995; 57 Grossmann, Roschitzki, Panse, Fortes, Barkow-Oesterreicher, Rutishauser, Schlapbach (bb0510) 2010; 73 Clough, Key, Ott, Ragg, Schadow, Vitek (bb0460) 2009; 8 Pavelka, Pelizzola, Vizzardelli, Capozzoli, Splendiani, Granucci, Ricciardi-Castagnoli (bb0300) 2004; 5 Dicker, Lin, Ivanov (bb0500) 2010; 9 Zybailov, Mosley, Sardiu, Coleman, Florens, Washburn (bb0170) 2006; 5 Choi, Kim, Fermin, Tsou, Nesvizhskii (bb0435) 2015; 129 Podwojski, Eisenacher, Kohl, Turewicz, Meyer, Rahnenführer, Stephan (bb0395) 2010; 7 Colaert, Vandekerckhove, Gevaert, Martens (bb0515) 2011; 11 Nesvizhskii (bb0035) 2010; 73 Zhang, Wen, Washburn, Florens (bb0205) 2010; 82 Lee, O'Connell (bb0325) 2003 Zhang, Fonslow, Shan, Baek, Yates (bb0010) 2013; 113 Krey, Wilmarth, Shin, Klimek, Sherman, Jeffery, Choi, David, Barr-Gillespie (bb0520) 2014; 13 Vogel, Marcotte (bb0190) 2012; 893 Braisted, Kuntumalla, Vogel, Marcotte, Rodrigues, Wang, Huang, Ferlanti, Saeed, Fleischmann, Peterson, Pieper (bb0195) 2008; 9 Washburn, Wolters, Yates (bb0055) 2001; 19 McIlwain, Mathews, Bereman, Rubel, MacCoss, Noble (bb0530) 2012; 13 Neilson, Ali, Muralidharan, Mirzaei, Mariani, Assadourian, Lee, van Sluyter, Haynes (bb0100) 2011; 11 Futcher, Latter, Monardo, McLaughlin, Garrels (bb0060) 1999; 19 Griffin, Yu, Long, Oh, Shore, Li, Koziol, Schnitzer (bb0230) 2010; 28 Clough, Thaminy, Ragg, Aebersold, Vitek (bb0465) 2012; 13 Tom Taverner (bb0480) 2012; 28 Jasna Beganović (bb0260) 2010; 9 Glish, Burinsky (bb0030) 2008; 19 Shalit, Elinger, Savidor, Gabashvili, Levin (bb0555) 2015; 14 Liu, Sadygov, Yates (bb0145) 2004; 76 Sun, Zhang, Wang, Yang, Wei, Zhu, Jiang, He (bb0140) 2009; 8 Ryu, Qian, Camp, Smith, Tompkins, Davis, Xiao (bb0485) 2014; 30 Rosenberger, Ludwig, Röst, Aebersold, Malmström (bb0200) 2014; 30 Blein-Nicolas, Xu, de Vienne, Giraud, Huet, Zivy (bb0090) 2012; 12 Nahnsen, Bielow, Reinert, Kohlbacher (bb0105) 2013; 12 Love, Huber, Anders (bb0355) 2014; 15 Wu, Zhao, Liang, Qu, Zhang, Zhang (bb0245) 2012; 137 Schwanhäusser, Busse, Li, Dittmar, Schuchhardt, Wolf, Chen, Selbach (bb0425) 2011; 473 Gao, Opiteck, Friedrichs, Dongre, Hefta (bb0155) 2003; 2 Arike, Valgepea, Peil, Nahku, Adamberg, Vilu (bb0550) 2012; 75 Kruskal, Wallis (bb0290) 1952; 47 Li, Gray, Zhang, Chung, Billheimer, Yarbrough, Liebler, Shyr, Slebos (bb0380) 2010; 9 Bukhman, Dharsee, Ewing, Chu, Topaloglou, Le Bihan, Goh, Duewel, Stewart, Wisniewski, Ng (bb0470) 2008; 6 Milac, Randolph, Wang (bb0545) 2012; 5 Dost, Bandeira, Li, Shen, Briggs, Bafna (bb0490) 2012; 19 Ahrné, Molzahn, Glatter, Schmidt (bb0505) 2013; 13 Smyth (bb0445) 2004; 3 Trudgian, Ridlova, Fischer, Mackeen, Ternette, Acuto, Kessler, Thomas (bb0235) 2011; 11 Lu, Vogel, Wang, Yao, Marcotte (bb0185) 2007; 25 Chen, Chambers, Li, Ham, Turner, Zhang, Tabb (bb0430) 2013; 12 Jaffe, Mani, Leptos, Church, Gillette, Carr (bb0410) 2006; 5 Lasonder, Ishihama, Andersen, Vermunt, Pain, Sauerwein, Eling, Hall, Waters, Stunnenberg, Mann (bb0220) 2002; 419 Cox, Hein, Luber, Paron, Nagaraj, Mann (bb0495) 2014; 13 Heinecke, Pratt, Vaisar, Becker (bb0365) 2010; 26 Pursiheimo, Vehmas, Afzal, Suomi, Chand, Strauss, Poutanen, Rokka, Corthals, Elo (bb0440) 2015; 14 Sokal, Rohlf (bb0275) 1995 Higgs, Knierman, Gelfanova, Butler, Hale (bb0400) 2005; 4 Student (bb0255) 1907; 5 Anders, Huber (bb0350) 2010; 11 Asara, Christofk, Freimark, Cantley (bb0225) 2008; 8 Carvalho, Fischer, Chen, Yates, Barbosa (bb0310) 2008; 9 Voyksner, Lee (bb0065) 1999; 13 Craig, Beavis (bb0040) 2004; 20 McIlwain, Tamura, Kertesz-Farkas, Grant, Diament, Frewen, Howbert, Hoopmann, Käll, Eng, MacCoss, Noble (bb0135) 2014; 13 Domon, Aebersold (bb0005) 2010; 28 Jain, Thatte, Braciale, Ley, O'Connell, Lee (bb0315) 2003; 19 Polpitiya, Qian, Jaitly, Petyuk, Adkins, Camp, Anderson, Smith (bb0415) 2008; 24 Tu, Li, Sheng, Zhang, Qu (bb0525) 2014; 13 Elo, Filén, Lahesmaa, Aittokallio (bb0455) 2008; 5 Lee (bb0320) 2001; 47 Searle (bb0130) 2010; 10 Gerster, Kwon, Ludwig, Matondo, Vogel, Marcotte, Aebersold, Bühlmann (bb0475) 2014; 13 Matzke, Brown, Gritsenko, Metz, Pounds, Rodland, Shukla, Smith, Waters, McDermott, Webb-Robertson (bb0110) 2013; 13 Rappsilber, Ryder, Lamond, Mann (bb0115) 2002; 12 Fisher (bb0270) 1925 Choi, Fermin, Nesvizhskii (bb0370) 2008; 7 Little, Lee, Ley (bb0330) 2010; 10 Fu, Gharib, Green, Aitken, Frazer, Park, Vaisar, Heinecke (bb0360) 2008; 7 Ning, Fermin, Nesvizhskii (bb0420) 2012; 11 Booth, Eilertson, Olinares, Yu (bb0375) 2011; 10 Li, Radivojac (bb0050) 2012; 13 Fermin, Basrur, Yocum, Nesvizhskii (bb0210) 2011; 11 Wu, Shan, Qu, Jiang, Yuan, Liu, Zhang, Liang, Zhang, Zhang (bb0250) 2014; 139 Student (10.1016/j.bbapap.2016.02.019_bb0255) 1907; 5 Ryu (10.1016/j.bbapap.2016.02.019_bb0485) 2014; 30 Higgs (10.1016/j.bbapap.2016.02.019_bb0400) 2005; 4 Dost (10.1016/j.bbapap.2016.02.019_bb0490) 2012; 19 Li (10.1016/j.bbapap.2016.02.019_bb0050) 2012; 13 Pursiheimo (10.1016/j.bbapap.2016.02.019_bb0440) 2015; 14 Pang (10.1016/j.bbapap.2016.02.019_bb0150) 2002; 1 Colaert (10.1016/j.bbapap.2016.02.019_bb0515) 2011; 11 Langley (10.1016/j.bbapap.2016.02.019_bb0340) 2015; 129 Chen (10.1016/j.bbapap.2016.02.019_bb0430) 2013; 12 Braisted (10.1016/j.bbapap.2016.02.019_bb0195) 2008; 9 Jasna Beganović (10.1016/j.bbapap.2016.02.019_bb0260) 2010; 9 Heinecke (10.1016/j.bbapap.2016.02.019_bb0365) 2010; 26 Polpitiya (10.1016/j.bbapap.2016.02.019_bb0415) 2008; 24 Bukhman (10.1016/j.bbapap.2016.02.019_bb0470) 2008; 6 Fermin (10.1016/j.bbapap.2016.02.019_bb0210) 2011; 11 Griffin (10.1016/j.bbapap.2016.02.019_bb0230) 2010; 28 Dicker (10.1016/j.bbapap.2016.02.019_bb0500) 2010; 9 Rardin (10.1016/j.bbapap.2016.02.019_bb0540) 2015; 14 Clough (10.1016/j.bbapap.2016.02.019_bb0460) 2009; 8 Wu (10.1016/j.bbapap.2016.02.019_bb0250) 2014; 139 Pham (10.1016/j.bbapap.2016.02.019_bb0265) 2010; 26 Gao (10.1016/j.bbapap.2016.02.019_bb0155) 2003; 2 Webb-Robertson (10.1016/j.bbapap.2016.02.019_bb0390) 2015; 14 Zybailov (10.1016/j.bbapap.2016.02.019_bb0170) 2006; 5 Zhang (10.1016/j.bbapap.2016.02.019_bb0205) 2010; 82 Arike (10.1016/j.bbapap.2016.02.019_bb0550) 2012; 75 Karpievitch (10.1016/j.bbapap.2016.02.019_bb0385) 2009; 25 Freund (10.1016/j.bbapap.2016.02.019_bb0535) 2013; 12 Grossmann (10.1016/j.bbapap.2016.02.019_bb0510) 2010; 73 McIlwain (10.1016/j.bbapap.2016.02.019_bb0135) 2014; 13 Pavelka (10.1016/j.bbapap.2016.02.019_bb0295) 2008; 7 Lee (10.1016/j.bbapap.2016.02.019_bb0325) 2003 Sokal (10.1016/j.bbapap.2016.02.019_bb0275) 1995 Blein-Nicolas (10.1016/j.bbapap.2016.02.019_bb0090) 2012; 12 Cox (10.1016/j.bbapap.2016.02.019_bb0080) 2008; 26 Lu (10.1016/j.bbapap.2016.02.019_bb0185) 2007; 25 Lundgren (10.1016/j.bbapap.2016.02.019_bb0215) 2010; 7 Matzke (10.1016/j.bbapap.2016.02.019_bb0110) 2013; 13 Lee (10.1016/j.bbapap.2016.02.019_bb0320) 2001; 47 Benjamini (10.1016/j.bbapap.2016.02.019_bb0345) 1995; 57 Rosenberger (10.1016/j.bbapap.2016.02.019_bb0200) 2014; 30 Krey (10.1016/j.bbapap.2016.02.019_bb0520) 2014; 13 Chelius (10.1016/j.bbapap.2016.02.019_bb0070) 2002; 1 Choi (10.1016/j.bbapap.2016.02.019_bb0370) 2008; 7 Asara (10.1016/j.bbapap.2016.02.019_bb0225) 2008; 8 Smyth (10.1016/j.bbapap.2016.02.019_bb0445) 2004; 3 Cox (10.1016/j.bbapap.2016.02.019_bb0495) 2014; 13 Silva (10.1016/j.bbapap.2016.02.019_bb0405) 2006; 5 Shalit (10.1016/j.bbapap.2016.02.019_bb0555) 2015; 14 Lasonder (10.1016/j.bbapap.2016.02.019_bb0220) 2002; 419 Li (10.1016/j.bbapap.2016.02.019_bb0380) 2010; 9 Pavelka (10.1016/j.bbapap.2016.02.019_bb0300) 2004; 5 Nesvizhskii (10.1016/j.bbapap.2016.02.019_bb0035) 2010; 73 Liu (10.1016/j.bbapap.2016.02.019_bb0145) 2004; 76 Shinoda (10.1016/j.bbapap.2016.02.019_bb0125) 2010; 26 Fu (10.1016/j.bbapap.2016.02.019_bb0360) 2008; 7 Zhang (10.1016/j.bbapap.2016.02.019_bb0010) 2013; 113 Powell (10.1016/j.bbapap.2016.02.019_bb0175) 2004; 24 Colaert (10.1016/j.bbapap.2016.02.019_bb0240) 2011; 10 Bilbao (10.1016/j.bbapap.2016.02.019_bb0020) 2015; 15 Fisher (10.1016/j.bbapap.2016.02.019_bb0270) 1925 Choi (10.1016/j.bbapap.2016.02.019_bb0435) 2015; 129 Rappsilber (10.1016/j.bbapap.2016.02.019_bb0115) 2002; 12 Kannaste (10.1016/j.bbapap.2016.02.019_bb0165) 2014; 13 Valot (10.1016/j.bbapap.2016.02.019_bb0075) 2011; 11 Audic (10.1016/j.bbapap.2016.02.019_bb0305) 1997; 7 Mann (10.1016/j.bbapap.2016.02.019_bb0285) 1947; 18 Sun (10.1016/j.bbapap.2016.02.019_bb0140) 2009; 8 Peng (10.1016/j.bbapap.2016.02.019_bb0180) 2004; 279 Kruskal (10.1016/j.bbapap.2016.02.019_bb0290) 1952; 47 Schwanhäusser (10.1016/j.bbapap.2016.02.019_bb0425) 2011; 473 Carvalho (10.1016/j.bbapap.2016.02.019_bb0310) 2008; 9 Ishihama (10.1016/j.bbapap.2016.02.019_bb0120) 2005; 4 Daly (10.1016/j.bbapap.2016.02.019_bb0095) 2008; 7 Jaffe (10.1016/j.bbapap.2016.02.019_bb0410) 2006; 5 Bourmaud (10.1016/j.bbapap.2016.02.019_bb0015) 2014 Hawkridge (10.1016/j.bbapap.2016.02.019_bb0025) 2014 Podwojski (10.1016/j.bbapap.2016.02.019_bb0395) 2010; 7 Ying Zhang (10.1016/j.bbapap.2016.02.019_bb0160) 2009; 81 Anders (10.1016/j.bbapap.2016.02.019_bb0350) 2010; 11 Nahnsen (10.1016/j.bbapap.2016.02.019_bb0105) 2013; 12 Trudgian (10.1016/j.bbapap.2016.02.019_bb0235) 2011; 11 Love (10.1016/j.bbapap.2016.02.019_bb0355) 2014; 15 Clough (10.1016/j.bbapap.2016.02.019_bb0465) 2012; 13 Booth (10.1016/j.bbapap.2016.02.019_bb0375) 2011; 10 Ahrné (10.1016/j.bbapap.2016.02.019_bb0505) 2013; 13 Glish (10.1016/j.bbapap.2016.02.019_bb0030) 2008; 19 Perkins (10.1016/j.bbapap.2016.02.019_bb0045) 1999; 20 Craig (10.1016/j.bbapap.2016.02.019_bb0040) 2004; 20 Gerster (10.1016/j.bbapap.2016.02.019_bb0475) 2014; 13 MacLean (10.1016/j.bbapap.2016.02.019_bb0085) 2010; 23 Vogel (10.1016/j.bbapap.2016.02.019_bb0190) 2012; 893 Futcher (10.1016/j.bbapap.2016.02.019_bb0060) 1999; 19 Elo (10.1016/j.bbapap.2016.02.019_bb0455) 2008; 5 Neilson (10.1016/j.bbapap.2016.02.019_bb0100) 2011; 11 Wu (10.1016/j.bbapap.2016.02.019_bb0245) 2012; 137 Jain (10.1016/j.bbapap.2016.02.019_bb0315) 2003; 19 Searle (10.1016/j.bbapap.2016.02.019_bb0130) 2010; 10 Voyksner (10.1016/j.bbapap.2016.02.019_bb0065) 1999; 13 Tu (10.1016/j.bbapap.2016.02.019_bb0525) 2014; 13 McIlwain (10.1016/j.bbapap.2016.02.019_bb0530) 2012; 13 Milac (10.1016/j.bbapap.2016.02.019_bb0545) 2012; 5 Little (10.1016/j.bbapap.2016.02.019_bb0330) 2010; 10 Domon (10.1016/j.bbapap.2016.02.019_bb0005) 2010; 28 Washburn (10.1016/j.bbapap.2016.02.019_bb0055) 2001; 19 Tusher (10.1016/j.bbapap.2016.02.019_bb0335) 2001; 98 Breitling (10.1016/j.bbapap.2016.02.019_bb0450) 2004; 573 Tom Taverner (10.1016/j.bbapap.2016.02.019_bb0480) 2012; 28 Zhang (10.1016/j.bbapap.2016.02.019_bb0280) 2006; 5 Ning (10.1016/j.bbapap.2016.02.019_bb0420) 2012; 11 |
| References_xml | – volume: 19 start-page: 1945 year: 2003 end-page: 1951 ident: bb0315 article-title: Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays publication-title: Bioinformatics contributor: fullname: Lee – volume: 8 start-page: 4934 year: 2009 end-page: 4942 ident: bb0140 article-title: Modified spectral count index (mSCI) for estimation of protein abundance by protein relative identification possibility (RIPpro): a new proteomic technological parameter publication-title: J. Proteome Res. contributor: fullname: He – volume: 13 start-page: 2567 year: 2013 end-page: 2578 ident: bb0505 article-title: Critical assessment of proteome-wide label-free absolute abundance estimation strategies publication-title: Proteomics contributor: fullname: Schmidt – volume: 137 start-page: 3146 year: 2012 end-page: 3153 ident: bb0245 article-title: NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification publication-title: Analyst contributor: fullname: Zhang – volume: 24 start-page: 1556 year: 2008 end-page: 1558 ident: bb0415 article-title: DAnTE: a statistical tool for quantitative analysis of -omics data publication-title: Bioinformatics contributor: fullname: Smith – volume: 8 start-page: 5275 year: 2009 end-page: 5284 ident: bb0460 article-title: Protein quantification in label-free LC–MS experiments publication-title: J. Proteome Res. contributor: fullname: Vitek – start-page: 163 year: 2003 end-page: 184 ident: bb0325 article-title: An S-PLUS library for the analysis of differential expression publication-title: The Analysis of Gene Expression Data: An Overview of Methods and Sofware contributor: fullname: O'Connell – volume: 12 start-page: 549 year: 2013 end-page: 556 ident: bb0105 article-title: Tools for label-free peptide quantification publication-title: Mol. Cell. Proteomics contributor: fullname: Kohlbacher – volume: 4 start-page: 1265 year: 2005 end-page: 1272 ident: bb0120 article-title: Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein publication-title: Mol. Cell. Proteomics contributor: fullname: Mann – volume: 26 start-page: 576 year: 2010 end-page: 577 ident: bb0125 article-title: emPAI Calc—for the estimation of protein abundance from large-scale identification data by liquid chromatography–tandem mass spectrometry publication-title: Bioinformatics contributor: fullname: Ishihama – volume: 19 start-page: 242 year: 2001 end-page: 247 ident: bb0055 article-title: Large-scale analysis of the yeast proteome by multidimensional protein identification technology publication-title: Nat. Biotechnol. contributor: fullname: Yates – volume: 28 start-page: 2404 year: 2012 end-page: 2406 ident: bb0480 article-title: DanteR: an extensible R-based tool for quantitative analysis of -omics data publication-title: Bioinformatics contributor: fullname: Tom Taverner – volume: 5 start-page: 1927 year: 2006 end-page: 1941 ident: bb0410 article-title: PEPPeR, a platform for experimental proteomic pattern recognition publication-title: Mol. Cell. Proteomics contributor: fullname: Carr – volume: 73 start-page: 2092 year: 2010 end-page: 2123 ident: bb0035 article-title: A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics publication-title: J. Proteomics contributor: fullname: Nesvizhskii – volume: 25 start-page: 2028 year: 2009 end-page: 2034 ident: bb0385 article-title: A statistical framework for protein quantitation in bottom-up MS-based proteomics publication-title: Bioinformatics contributor: fullname: Dabney – volume: 12 start-page: 4111 year: 2013 end-page: 4121 ident: bb0430 article-title: IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification publication-title: J. Proteome Res. contributor: fullname: Tabb – volume: 10 start-page: 1212 year: 2010 end-page: 1222 ident: bb0330 article-title: ReSASC: a resampling-based algorithm to determine differential protein expression from spectral count data publication-title: Proteomics contributor: fullname: Ley – volume: 13 start-page: 1034 year: 2014 end-page: 1044 ident: bb0520 article-title: Accurate label-free protein quantitation with high- and low-resolution mass spectrometers publication-title: J. Proteome Res. contributor: fullname: Barr-Gillespie – volume: 13 start-page: 1957 year: 2014 end-page: 1968 ident: bb0165 article-title: Cross-correlation of spectral count ranking to validate quantitative proteome measurements publication-title: J. Proteome Res. contributor: fullname: Corthals – year: 1925 ident: bb0270 article-title: Statistical Methods for Research Workers contributor: fullname: Fisher – volume: 9 start-page: 529 year: 2008 ident: bb0195 article-title: The APEX quantitative proteomics tool: generating protein quantitation estimates from LC–MS/MS proteomics results publication-title: BMC Bioinf. contributor: fullname: Pieper – volume: 7 start-page: 845 year: 2008 end-page: 854 ident: bb0360 article-title: Spectral index for assessment of differential protein expression in shotgun proteomics publication-title: J. Proteome Res. contributor: fullname: Heinecke – volume: 23 start-page: 488 year: 2010 end-page: 493 ident: bb0085 article-title: Predicting epistasis: an experimental test of metabolic control theory with bacterial transcription and translation publication-title: J. Evol. Biol. contributor: fullname: MacLean – volume: 13 start-page: S4 year: 2012 ident: bb0050 article-title: Computational approaches to protein inference in shotgun proteomics publication-title: BMC Bioinf. contributor: fullname: Radivojac – volume: 13 start-page: 308 year: 2012 ident: bb0530 article-title: Estimating relative abundances of proteins from shotgun proteomics data publication-title: BMC Bioinf. contributor: fullname: Noble – volume: 24 start-page: 7249 year: 2004 end-page: 7259 ident: bb0175 article-title: Cluster analysis of mass spectrometry data reveals a novel component of SAGA publication-title: Mol. Cell. Biol. contributor: fullname: Link – volume: 13 start-page: S6 year: 2012 ident: bb0465 article-title: Statistical protein quantification and significance analysis in label-free LC–MS experiments with complex designs publication-title: BMC Bioinf. contributor: fullname: Vitek – volume: 13 start-page: 666 year: 2014 end-page: 677 ident: bb0475 article-title: Statistical approach to protein quantification publication-title: Mol. Cell. Proteomics contributor: fullname: Bühlmann – volume: 5 start-page: 351 year: 1907 end-page: 360 ident: bb0255 article-title: On the error of counting with a haemacytometer publication-title: Biometrika contributor: fullname: Student – volume: 19 start-page: 7357 year: 1999 end-page: 7368 ident: bb0060 article-title: A sampling of the yeast proteome publication-title: Mol. Cell. Biol. contributor: fullname: Garrels – volume: 7 start-page: 39 year: 2010 end-page: 53 ident: bb0215 article-title: Role of spectral counting in quantitative proteomics publication-title: Expert Rev. Proteomics contributor: fullname: Han – volume: 11 start-page: 3572 year: 2011 end-page: 3577 ident: bb0075 article-title: MassChroQ publication-title: Proteomics contributor: fullname: Zivy – volume: 5 start-page: 423 year: 2008 end-page: 431 ident: bb0455 article-title: Reproducibility-optimized test statistic for ranking genes in microarray studies publication-title: IEEE/ACM Trans. Comput. Biol. Bioinform. contributor: fullname: Aittokallio – volume: 573 start-page: 83 year: 2004 end-page: 92 ident: bb0450 article-title: Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments publication-title: FEBS Lett. contributor: fullname: Herzyk – volume: 11 start-page: 1340 year: 2011 end-page: 1345 ident: bb0210 article-title: Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis publication-title: Proteomics contributor: fullname: Nesvizhskii – volume: 81 start-page: 6317 year: 2009 end-page: 6326 ident: bb0160 article-title: Effect of dynamic exclusion duration on spectral count based quantitative proteomics publication-title: Anal. Chem. contributor: fullname: Ying Zhang – year: 1995 ident: bb0275 article-title: Biometry contributor: fullname: Rohlf – volume: 473 start-page: 337 year: 2011 end-page: 342 ident: bb0425 article-title: Global quantification of mammalian gene expression control publication-title: Nature contributor: fullname: Selbach – volume: 5 start-page: 144 year: 2006 end-page: 156 ident: bb0405 article-title: Absolute quantification of proteins by LCMSE a virtue of parallel ms acquisition publication-title: Mol. Cell. Proteomics contributor: fullname: Geromanos – volume: 15 start-page: 964 year: 2015 end-page: 980 ident: bb0020 article-title: Processing strategies and software solutions for data-independent acquisition in mass spectrometry publication-title: Proteomics contributor: fullname: Lisacek – volume: 893 start-page: 321 year: 2012 end-page: 341 ident: bb0190 article-title: Label-free protein quantitation using weighted spectral counting publication-title: Methods Mol. Biol. contributor: fullname: Marcotte – volume: 26 start-page: 1574 year: 2010 end-page: 1575 ident: bb0365 article-title: PepC: proteomics software for identifying differentially expressed proteins based on spectral counting publication-title: Bioinformatics contributor: fullname: Becker – volume: 13 start-page: 493 year: 2013 end-page: 503 ident: bb0110 article-title: A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC–MS proteomics experiments publication-title: Proteomics contributor: fullname: Webb-Robertson – volume: 5 start-page: 2339 year: 2006 end-page: 2347 ident: bb0170 article-title: Statistical analysis of membrane proteome expression changes in publication-title: J. Proteome Res. contributor: fullname: Washburn – volume: 419 start-page: 537 year: 2002 end-page: 542 ident: bb0220 article-title: Analysis of the publication-title: Nature contributor: fullname: Mann – volume: 26 start-page: 1367 year: 2008 end-page: 1372 ident: bb0080 article-title: MaxQuant enables high peptide identification rates, individualized p.p.b-range mass accuracies and proteome-wide protein quantification publication-title: Nat. Biotechnol. contributor: fullname: Mann – volume: 9 start-page: 677 year: 2010 end-page: 688 ident: bb0260 article-title: Characterization of the insoluble proteome of publication-title: J. Proteome Res. contributor: fullname: Jasna Beganović – volume: 279 start-page: 21003 year: 2004 end-page: 21011 ident: bb0180 article-title: Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry publication-title: J. Biol. Chem. contributor: fullname: Sheng – volume: 13 start-page: 2513 year: 2014 end-page: 2526 ident: bb0495 article-title: Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ publication-title: Mol. Cell. Proteomics contributor: fullname: Mann – volume: 13 start-page: 2069 year: 2014 end-page: 2079 ident: bb0525 article-title: Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data publication-title: J. Proteome Res. contributor: fullname: Qu – volume: 7 start-page: 2373 year: 2008 end-page: 2385 ident: bb0370 article-title: Significance analysis of spectral count data in label-free shotgun proteomics publication-title: Mol. Cell. Proteomics contributor: fullname: Nesvizhskii – volume: 14 start-page: 1979 year: 2015 end-page: 1986 ident: bb0555 article-title: MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer publication-title: J. Proteome Res. contributor: fullname: Levin – volume: 8 start-page: 994 year: 2008 end-page: 999 ident: bb0225 article-title: A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen publication-title: Proteomics contributor: fullname: Cantley – volume: 98 start-page: 5116 year: 2001 end-page: 5121 ident: bb0335 article-title: Significance analysis of microarrays applied to the ionizing radiation response publication-title: Proc. Natl. Acad. Sci. U. S. A. contributor: fullname: Chu – volume: 82 start-page: 2272 year: 2010 end-page: 2281 ident: bb0205 article-title: Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins publication-title: Anal. Chem. contributor: fullname: Florens – volume: 14 start-page: 1993 year: 2015 end-page: 2001 ident: bb0390 article-title: Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics publication-title: J. Proteome Res. contributor: fullname: Waters – volume: 7 start-page: 986 year: 1997 end-page: 995 ident: bb0305 article-title: The significance of digital gene expression profiles publication-title: Genome Res. contributor: fullname: Claverie – volume: 1 start-page: 317 year: 2002 end-page: 323 ident: bb0070 article-title: Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry publication-title: J. Proteome Res. contributor: fullname: Bondarenko – volume: 9 start-page: 4295 year: 2010 end-page: 4305 ident: bb0380 article-title: Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling publication-title: J. Proteome Res. contributor: fullname: Slebos – volume: 47 start-page: 1350 year: 2001 end-page: 1352 ident: bb0320 article-title: Analysis issues for gene expression array data publication-title: Clin. Chem. contributor: fullname: Lee – volume: 1 start-page: 161 year: 2002 end-page: 169 ident: bb0150 article-title: Biomarker discovery in urine by proteomics publication-title: J. Proteome Res. contributor: fullname: Opiteck – volume: 20 start-page: 3551 year: 1999 end-page: 3567 ident: bb0045 article-title: Probability-based protein identification by searching sequence databases using mass spectrometry data publication-title: Eletrophoresis contributor: fullname: Cottrell – volume: 4 start-page: 1442 year: 2005 end-page: 1450 ident: bb0400 article-title: Comprehensive label-free method for the relative quantification of proteins from biological samples publication-title: J. Proteome Res. contributor: fullname: Hale – volume: 3 year: 2004 ident: bb0445 article-title: Linear models and empirical bayes methods for assessing differential expression in microarray experiments publication-title: Stat. Appl. Genet. Mol. Biol. contributor: fullname: Smyth – volume: 2 start-page: 643 year: 2003 end-page: 649 ident: bb0155 article-title: Changes in the protein expression of yeast as a function of carbon source publication-title: J. Proteome Res. contributor: fullname: Hefta – volume: 76 start-page: 4193 year: 2004 end-page: 4201 ident: bb0145 article-title: A model for random sampling and estimation of relative protein abundance in shotgun proteomics publication-title: Anal. Chem. contributor: fullname: Yates – volume: 5 start-page: 2909 year: 2006 end-page: 2918 ident: bb0280 article-title: Detecting differential and correlated protein expression in label-free shotgun proteomics publication-title: J. Proteome Res. contributor: fullname: Samatova – volume: 75 start-page: 5437 year: 2012 end-page: 5448 ident: bb0550 article-title: Comparison and applications of label-free absolute proteome quantification methods on publication-title: J. Proteomics contributor: fullname: Vilu – volume: 11 start-page: 2790 year: 2011 end-page: 2797 ident: bb0235 article-title: Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline publication-title: Proteomics contributor: fullname: Thomas – volume: 18 start-page: 50 year: 1947 end-page: 60 ident: bb0285 article-title: On a test of whether one of two random variables is stochastically larger than the other publication-title: Ann. Math. Stat. contributor: fullname: Whitney – volume: 7 start-page: 631 year: 2008 end-page: 644 ident: bb0295 article-title: Statistical similarities between transcriptomics and quantitative shotgun proteomics data publication-title: Mol. Cell. Proteomics contributor: fullname: Washburn – volume: 113 start-page: 2343 year: 2013 end-page: 2394 ident: bb0010 article-title: Protein analysis by shotgun/bottom-up proteomics publication-title: Chem. Rev. contributor: fullname: Yates – volume: 7 start-page: 249 year: 2010 end-page: 261 ident: bb0395 article-title: Peek a peak: a glance at statistics for quantitative label-free proteomics publication-title: Expert Rev. Proteomics contributor: fullname: Stephan – volume: 6 start-page: 107 year: 2008 end-page: 123 ident: bb0470 article-title: Design and analysis of quantitative differential proteomics investigations using LC–MS technology publication-title: J. Bioinform. Comput. Biol. contributor: fullname: Ng – volume: 47 start-page: 583 year: 1952 end-page: 621 ident: bb0290 article-title: Use of ranks in one-criterion variance analysis publication-title: J. Am. Stat. Assoc. contributor: fullname: Wallis – volume: 10 year: 2011 ident: bb0375 article-title: A bayesian mixture model for comparative spectral count data in shotgun proteomics publication-title: Mol. Cell. Proteomics contributor: fullname: Yu – volume: 57 start-page: 289 year: 1995 end-page: 300 ident: bb0345 article-title: Controlling the false discovery rate: a practical and powerful approach to multiple testing publication-title: J. R. Stat. Soc. Ser. B Methodol. contributor: fullname: Hochberg – volume: 15 start-page: 550 year: 2014 ident: bb0355 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 publication-title: Genome Biol. contributor: fullname: Anders – volume: 11 start-page: R106 year: 2010 ident: bb0350 article-title: Differential expression analysis for sequence count data publication-title: Genome Biol. contributor: fullname: Huber – volume: 14 start-page: 2405 year: 2015 end-page: 2419 ident: bb0540 article-title: MS1 peptide ion intensity chromatograms in MS2 (SWATH) data independent acquisitions improving post acquisition analysis of proteomic experiments publication-title: Mol. Cell. Proteomics contributor: fullname: Gibson – volume: 19 start-page: 161 year: 2008 end-page: 172 ident: bb0030 article-title: Hybrid mass spectrometers for tandem mass spectrometry publication-title: J. Am. Soc. Mass Spectrom. contributor: fullname: Burinsky – volume: 12 start-page: 1231 year: 2002 end-page: 1245 ident: bb0115 article-title: Large-scale proteomic analysis of the human spliceosome publication-title: Genome Res. contributor: fullname: Mann – volume: 28 start-page: 710 year: 2010 end-page: 721 ident: bb0005 article-title: Options and considerations when selecting a quantitative proteomics strategy publication-title: Nat. Biotechnol. contributor: fullname: Aebersold – volume: 12 start-page: 2797 year: 2012 end-page: 2801 ident: bb0090 article-title: Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics publication-title: Proteomics contributor: fullname: Zivy – volume: 11 start-page: 1110 year: 2011 end-page: 1113 ident: bb0515 article-title: A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision publication-title: Proteomics contributor: fullname: Martens – volume: 28 start-page: 83 year: 2010 end-page: 89 ident: bb0230 article-title: Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis publication-title: Nat. Biotechnol. contributor: fullname: Schnitzer – volume: 11 start-page: 535 year: 2011 end-page: 553 ident: bb0100 article-title: Less label, more free: approaches in label-free quantitative mass spectrometry publication-title: Proteomics contributor: fullname: Haynes – volume: 5 start-page: 75 year: 2012 end-page: 87 ident: bb0545 article-title: Analyzing LC–MS/MS data by spectral count and ion abundance: two case studies publication-title: Stat Interface contributor: fullname: Wang – start-page: 3 year: 2014 end-page: 25 ident: bb0025 article-title: Practical considerations and current limitations in quantitative mass spectrometry-based proteomics publication-title: Quantitative Proteomics contributor: fullname: Hawkridge – volume: 12 start-page: 1996 year: 2013 end-page: 2004 ident: bb0535 article-title: Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current publication-title: J. Proteome Res. contributor: fullname: Prenni – volume: 25 start-page: 117 year: 2007 end-page: 124 ident: bb0185 article-title: Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation publication-title: Nat. Biotechnol. contributor: fullname: Marcotte – volume: 30 start-page: 2741 year: 2014 end-page: 2746 ident: bb0485 article-title: Detecting differential protein expression in large-scale population proteomics publication-title: Bioinformatics contributor: fullname: Xiao – volume: 129 start-page: 83 year: 2015 end-page: 92 ident: bb0340 article-title: Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics publication-title: J. Proteomics contributor: fullname: Mayr – volume: 7 start-page: 1209 year: 2008 end-page: 1217 ident: bb0095 article-title: Mixed-effects statistical model for comparative LC–MS proteomics studies publication-title: J. Proteome Res. contributor: fullname: Baker – volume: 9 start-page: 2704 year: 2010 end-page: 2718 ident: bb0500 article-title: Increased power for the analysis of label-free LC–MS/MS proteomics data by combining spectral counts and peptide peak attributes publication-title: Mol. Cell. Proteomics contributor: fullname: Ivanov – volume: 26 start-page: 363 year: 2010 end-page: 369 ident: bb0265 article-title: On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics publication-title: Bioinformatics contributor: fullname: Jimenez – volume: 9 start-page: 316 year: 2008 ident: bb0310 article-title: PatternLab for proteomics: a tool for differential shotgun proteomics publication-title: BMC Bioinf. contributor: fullname: Barbosa – start-page: 26 year: 2014 end-page: 47 ident: bb0015 article-title: High resolution/accurate mass targeted proteomics publication-title: Quantitative Proteomics contributor: fullname: Domon – volume: 30 start-page: 2511 year: 2014 end-page: 2513 ident: bb0200 article-title: aLFQ: an R-package for estimating absolute protein quantities from label-free LC–MS/MS proteomics data publication-title: Bioinformatics contributor: fullname: Malmström – volume: 19 start-page: 337 year: 2012 end-page: 348 ident: bb0490 article-title: Accurate mass spectrometry based protein quantification via shared peptides publication-title: J. Comput. Biol. contributor: fullname: Bafna – volume: 14 start-page: 4118 year: 2015 end-page: 4126 ident: bb0440 article-title: Optimization of statistical methods impact on quantitative proteomics data publication-title: J. Proteome Res. contributor: fullname: Elo – volume: 10 start-page: 1265 year: 2010 end-page: 1269 ident: bb0130 article-title: Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies publication-title: Proteomics contributor: fullname: Searle – volume: 11 start-page: 2261 year: 2012 end-page: 2271 ident: bb0420 article-title: Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-seq gene expression data publication-title: J. Proteome Res. contributor: fullname: Nesvizhskii – volume: 139 start-page: 138 year: 2014 end-page: 146 ident: bb0250 article-title: Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current publication-title: Analyst contributor: fullname: Zhang – volume: 13 start-page: 1427 year: 1999 end-page: 1437 ident: bb0065 article-title: Investigating the use of an octupole ion guide for ion storage and high-pass mass filtering to improve the quantitative performance of electrospray ion trap mass spectrometry publication-title: Rapid Commun. Mass Spectrom. contributor: fullname: Lee – volume: 20 start-page: 1466 year: 2004 end-page: 1467 ident: bb0040 article-title: TANDEM: matching proteins with tandem mass spectra publication-title: Bioinformatics contributor: fullname: Beavis – volume: 10 start-page: 3183 year: 2011 end-page: 3189 ident: bb0240 article-title: RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification publication-title: J. Proteome Res. contributor: fullname: Martens – volume: 13 start-page: 4488 year: 2014 end-page: 4491 ident: bb0135 article-title: Crux: rapid open source protein tandem mass spectrometry analysis publication-title: J. Proteome Res. contributor: fullname: Noble – volume: 129 start-page: 121 year: 2015 end-page: 126 ident: bb0435 article-title: QPROT: statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics publication-title: J. Proteomics contributor: fullname: Nesvizhskii – volume: 73 start-page: 1740 year: 2010 end-page: 1746 ident: bb0510 article-title: Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods publication-title: J. Proteomics contributor: fullname: Schlapbach – volume: 5 start-page: 203 year: 2004 ident: bb0300 article-title: A power law global error model for the identification of differentially expressed genes in microarray data publication-title: BMC Bioinf. contributor: fullname: Ricciardi-Castagnoli – volume: 13 start-page: 4488 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0135 article-title: Crux: rapid open source protein tandem mass spectrometry analysis publication-title: J. Proteome Res. doi: 10.1021/pr500741y contributor: fullname: McIlwain – volume: 11 start-page: 1110 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0515 article-title: A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision publication-title: Proteomics doi: 10.1002/pmic.201000521 contributor: fullname: Colaert – volume: 14 start-page: 4118 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0440 article-title: Optimization of statistical methods impact on quantitative proteomics data publication-title: J. Proteome Res. doi: 10.1021/acs.jproteome.5b00183 contributor: fullname: Pursiheimo – volume: 10 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0375 article-title: A bayesian mixture model for comparative spectral count data in shotgun proteomics publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M110.007203 contributor: fullname: Booth – volume: 5 start-page: 351 year: 1907 ident: 10.1016/j.bbapap.2016.02.019_bb0255 article-title: On the error of counting with a haemacytometer publication-title: Biometrika doi: 10.1093/biomet/5.3.351 contributor: fullname: Student – volume: 11 start-page: 3572 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0075 article-title: MassChroQ: a versatile tool for mass spectrometry quantification publication-title: Proteomics doi: 10.1002/pmic.201100120 contributor: fullname: Valot – volume: 3 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0445 article-title: Linear models and empirical bayes methods for assessing differential expression in microarray experiments publication-title: Stat. Appl. Genet. Mol. Biol. doi: 10.2202/1544-6115.1027 contributor: fullname: Smyth – volume: 6 start-page: 107 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0470 article-title: Design and analysis of quantitative differential proteomics investigations using LC–MS technology publication-title: J. Bioinform. Comput. Biol. doi: 10.1142/S0219720008003321 contributor: fullname: Bukhman – volume: 19 start-page: 161 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0030 article-title: Hybrid mass spectrometers for tandem mass spectrometry publication-title: J. Am. Soc. Mass Spectrom. doi: 10.1016/j.jasms.2007.11.013 contributor: fullname: Glish – volume: 10 start-page: 1265 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0130 article-title: Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies publication-title: Proteomics doi: 10.1002/pmic.200900437 contributor: fullname: Searle – volume: 13 start-page: S4 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0050 article-title: Computational approaches to protein inference in shotgun proteomics publication-title: BMC Bioinf. doi: 10.1186/1471-2105-13-S16-S4 contributor: fullname: Li – volume: 7 start-page: 2373 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0370 article-title: Significance analysis of spectral count data in label-free shotgun proteomics publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M800203-MCP200 contributor: fullname: Choi – volume: 8 start-page: 4934 year: 2009 ident: 10.1016/j.bbapap.2016.02.019_bb0140 article-title: Modified spectral count index (mSCI) for estimation of protein abundance by protein relative identification possibility (RIPpro): a new proteomic technological parameter publication-title: J. Proteome Res. doi: 10.1021/pr900252n contributor: fullname: Sun – volume: 893 start-page: 321 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0190 article-title: Label-free protein quantitation using weighted spectral counting publication-title: Methods Mol. Biol. doi: 10.1007/978-1-61779-885-6_20 contributor: fullname: Vogel – volume: 7 start-page: 986 year: 1997 ident: 10.1016/j.bbapap.2016.02.019_bb0305 article-title: The significance of digital gene expression profiles publication-title: Genome Res. doi: 10.1101/gr.7.10.986 contributor: fullname: Audic – volume: 26 start-page: 1367 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0080 article-title: MaxQuant enables high peptide identification rates, individualized p.p.b-range mass accuracies and proteome-wide protein quantification publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1511 contributor: fullname: Cox – volume: 11 start-page: 535 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0100 article-title: Less label, more free: approaches in label-free quantitative mass spectrometry publication-title: Proteomics doi: 10.1002/pmic.201000553 contributor: fullname: Neilson – volume: 11 start-page: 2790 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0235 article-title: Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline publication-title: Proteomics doi: 10.1002/pmic.201000800 contributor: fullname: Trudgian – volume: 30 start-page: 2511 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0200 article-title: aLFQ: an R-package for estimating absolute protein quantities from label-free LC–MS/MS proteomics data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu200 contributor: fullname: Rosenberger – volume: 5 start-page: 203 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0300 article-title: A power law global error model for the identification of differentially expressed genes in microarray data publication-title: BMC Bioinf. doi: 10.1186/1471-2105-5-203 contributor: fullname: Pavelka – volume: 9 start-page: 529 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0195 article-title: The APEX quantitative proteomics tool: generating protein quantitation estimates from LC–MS/MS proteomics results publication-title: BMC Bioinf. doi: 10.1186/1471-2105-9-529 contributor: fullname: Braisted – volume: 26 start-page: 363 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0265 article-title: On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp677 contributor: fullname: Pham – volume: 11 start-page: R106 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0350 article-title: Differential expression analysis for sequence count data publication-title: Genome Biol. doi: 10.1186/gb-2010-11-10-r106 contributor: fullname: Anders – volume: 419 start-page: 537 year: 2002 ident: 10.1016/j.bbapap.2016.02.019_bb0220 article-title: Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry publication-title: Nature doi: 10.1038/nature01111 contributor: fullname: Lasonder – volume: 13 start-page: 1427 year: 1999 ident: 10.1016/j.bbapap.2016.02.019_bb0065 article-title: Investigating the use of an octupole ion guide for ion storage and high-pass mass filtering to improve the quantitative performance of electrospray ion trap mass spectrometry publication-title: Rapid Commun. Mass Spectrom. doi: 10.1002/(SICI)1097-0231(19990730)13:14<1427::AID-RCM662>3.0.CO;2-5 contributor: fullname: Voyksner – volume: 9 start-page: 677 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0260 article-title: Characterization of the insoluble proteome of Lactococcus lactis by SDS-PAGE LC–MS/MS leads to the identification of new markers of adaptation of the bacteria to the mouse digestive tract publication-title: J. Proteome Res. doi: 10.1021/pr9000866 contributor: fullname: Jasna Beganović – volume: 13 start-page: S6 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0465 article-title: Statistical protein quantification and significance analysis in label-free LC–MS experiments with complex designs publication-title: BMC Bioinf. doi: 10.1186/1471-2105-13-S16-S6 contributor: fullname: Clough – volume: 473 start-page: 337 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0425 article-title: Global quantification of mammalian gene expression control publication-title: Nature doi: 10.1038/nature10098 contributor: fullname: Schwanhäusser – year: 1925 ident: 10.1016/j.bbapap.2016.02.019_bb0270 contributor: fullname: Fisher – volume: 19 start-page: 1945 year: 2003 ident: 10.1016/j.bbapap.2016.02.019_bb0315 article-title: Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg264 contributor: fullname: Jain – start-page: 26 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0015 article-title: High resolution/accurate mass targeted proteomics contributor: fullname: Bourmaud – volume: 5 start-page: 75 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0545 article-title: Analyzing LC–MS/MS data by spectral count and ion abundance: two case studies publication-title: Stat Interface doi: 10.4310/SII.2012.v5.n1.a7 contributor: fullname: Milac – volume: 129 start-page: 83 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0340 article-title: Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics publication-title: J. Proteomics doi: 10.1016/j.jprot.2015.07.012 contributor: fullname: Langley – volume: 13 start-page: 1957 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0165 article-title: Cross-correlation of spectral count ranking to validate quantitative proteome measurements publication-title: J. Proteome Res. doi: 10.1021/pr401096z contributor: fullname: Kannaste – volume: 28 start-page: 710 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0005 article-title: Options and considerations when selecting a quantitative proteomics strategy publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1661 contributor: fullname: Domon – volume: 15 start-page: 550 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0355 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 publication-title: Genome Biol. doi: 10.1186/s13059-014-0550-8 contributor: fullname: Love – volume: 5 start-page: 144 year: 2006 ident: 10.1016/j.bbapap.2016.02.019_bb0405 article-title: Absolute quantification of proteins by LCMSE a virtue of parallel ms acquisition publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M500230-MCP200 contributor: fullname: Silva – volume: 73 start-page: 2092 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0035 article-title: A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics publication-title: J. Proteomics doi: 10.1016/j.jprot.2010.08.009 contributor: fullname: Nesvizhskii – volume: 18 start-page: 50 year: 1947 ident: 10.1016/j.bbapap.2016.02.019_bb0285 article-title: On a test of whether one of two random variables is stochastically larger than the other publication-title: Ann. Math. Stat. doi: 10.1214/aoms/1177730491 contributor: fullname: Mann – volume: 573 start-page: 83 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0450 article-title: Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments publication-title: FEBS Lett. doi: 10.1016/j.febslet.2004.07.055 contributor: fullname: Breitling – volume: 13 start-page: 2513 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0495 article-title: Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M113.031591 contributor: fullname: Cox – volume: 7 start-page: 39 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0215 article-title: Role of spectral counting in quantitative proteomics publication-title: Expert Rev. Proteomics doi: 10.1586/epr.09.69 contributor: fullname: Lundgren – volume: 7 start-page: 249 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0395 article-title: Peek a peak: a glance at statistics for quantitative label-free proteomics publication-title: Expert Rev. Proteomics doi: 10.1586/epr.09.107 contributor: fullname: Podwojski – volume: 14 start-page: 1979 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0555 article-title: MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer publication-title: J. Proteome Res. doi: 10.1021/pr501045t contributor: fullname: Shalit – volume: 8 start-page: 994 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0225 article-title: A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen publication-title: Proteomics doi: 10.1002/pmic.200700426 contributor: fullname: Asara – volume: 279 start-page: 21003 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0180 article-title: Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry publication-title: J. Biol. Chem. doi: 10.1074/jbc.M400103200 contributor: fullname: Peng – volume: 4 start-page: 1265 year: 2005 ident: 10.1016/j.bbapap.2016.02.019_bb0120 article-title: Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M500061-MCP200 contributor: fullname: Ishihama – volume: 12 start-page: 4111 year: 2013 ident: 10.1016/j.bbapap.2016.02.019_bb0430 article-title: IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification publication-title: J. Proteome Res. doi: 10.1021/pr400438q contributor: fullname: Chen – volume: 13 start-page: 308 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0530 article-title: Estimating relative abundances of proteins from shotgun proteomics data publication-title: BMC Bioinf. doi: 10.1186/1471-2105-13-308 contributor: fullname: McIlwain – start-page: 3 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0025 article-title: Practical considerations and current limitations in quantitative mass spectrometry-based proteomics contributor: fullname: Hawkridge – volume: 14 start-page: 2405 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0540 article-title: MS1 peptide ion intensity chromatograms in MS2 (SWATH) data independent acquisitions improving post acquisition analysis of proteomic experiments publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.O115.048181 contributor: fullname: Rardin – volume: 19 start-page: 7357 year: 1999 ident: 10.1016/j.bbapap.2016.02.019_bb0060 article-title: A sampling of the yeast proteome publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.19.11.7357 contributor: fullname: Futcher – volume: 12 start-page: 2797 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0090 article-title: Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics publication-title: Proteomics doi: 10.1002/pmic.201100660 contributor: fullname: Blein-Nicolas – volume: 13 start-page: 2069 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0525 article-title: Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data publication-title: J. Proteome Res. doi: 10.1021/pr401206m contributor: fullname: Tu – volume: 12 start-page: 1231 year: 2002 ident: 10.1016/j.bbapap.2016.02.019_bb0115 article-title: Large-scale proteomic analysis of the human spliceosome publication-title: Genome Res. doi: 10.1101/gr.473902 contributor: fullname: Rappsilber – volume: 7 start-page: 845 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0360 article-title: Spectral index for assessment of differential protein expression in shotgun proteomics publication-title: J. Proteome Res. doi: 10.1021/pr070271+ contributor: fullname: Fu – volume: 25 start-page: 117 year: 2007 ident: 10.1016/j.bbapap.2016.02.019_bb0185 article-title: Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation publication-title: Nat. Biotechnol. doi: 10.1038/nbt1270 contributor: fullname: Lu – volume: 9 start-page: 4295 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0380 article-title: Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling publication-title: J. Proteome Res. doi: 10.1021/pr100527g contributor: fullname: Li – volume: 30 start-page: 2741 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0485 article-title: Detecting differential protein expression in large-scale population proteomics publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu341 contributor: fullname: Ryu – volume: 19 start-page: 242 year: 2001 ident: 10.1016/j.bbapap.2016.02.019_bb0055 article-title: Large-scale analysis of the yeast proteome by multidimensional protein identification technology publication-title: Nat. Biotechnol. doi: 10.1038/85686 contributor: fullname: Washburn – volume: 76 start-page: 4193 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0145 article-title: A model for random sampling and estimation of relative protein abundance in shotgun proteomics publication-title: Anal. Chem. doi: 10.1021/ac0498563 contributor: fullname: Liu – volume: 7 start-page: 631 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0295 article-title: Statistical similarities between transcriptomics and quantitative shotgun proteomics data publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M700240-MCP200 contributor: fullname: Pavelka – volume: 20 start-page: 1466 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0040 article-title: TANDEM: matching proteins with tandem mass spectra publication-title: Bioinformatics doi: 10.1093/bioinformatics/bth092 contributor: fullname: Craig – volume: 19 start-page: 337 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0490 article-title: Accurate mass spectrometry based protein quantification via shared peptides publication-title: J. Comput. Biol. doi: 10.1089/cmb.2009.0267 contributor: fullname: Dost – volume: 10 start-page: 1212 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0330 article-title: ReSASC: a resampling-based algorithm to determine differential protein expression from spectral count data publication-title: Proteomics doi: 10.1002/pmic.200900328 contributor: fullname: Little – volume: 10 start-page: 3183 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0240 article-title: RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification publication-title: J. Proteome Res. doi: 10.1021/pr200219x contributor: fullname: Colaert – volume: 23 start-page: 488 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0085 article-title: Predicting epistasis: an experimental test of metabolic control theory with bacterial transcription and translation publication-title: J. Evol. Biol. doi: 10.1111/j.1420-9101.2009.01888.x contributor: fullname: MacLean – volume: 7 start-page: 1209 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0095 article-title: Mixed-effects statistical model for comparative LC–MS proteomics studies publication-title: J. Proteome Res. doi: 10.1021/pr070441i contributor: fullname: Daly – volume: 11 start-page: 1340 year: 2011 ident: 10.1016/j.bbapap.2016.02.019_bb0210 article-title: Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis publication-title: Proteomics doi: 10.1002/pmic.201000650 contributor: fullname: Fermin – volume: 47 start-page: 1350 year: 2001 ident: 10.1016/j.bbapap.2016.02.019_bb0320 article-title: Analysis issues for gene expression array data publication-title: Clin. Chem. doi: 10.1093/clinchem/47.8.1350 contributor: fullname: Lee – volume: 15 start-page: 964 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0020 article-title: Processing strategies and software solutions for data-independent acquisition in mass spectrometry publication-title: Proteomics doi: 10.1002/pmic.201400323 contributor: fullname: Bilbao – volume: 129 start-page: 121 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0435 article-title: QPROT: statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics publication-title: J. Proteomics doi: 10.1016/j.jprot.2015.07.036 contributor: fullname: Choi – volume: 2 start-page: 643 year: 2003 ident: 10.1016/j.bbapap.2016.02.019_bb0155 article-title: Changes in the protein expression of yeast as a function of carbon source publication-title: J. Proteome Res. doi: 10.1021/pr034038x contributor: fullname: Gao – volume: 4 start-page: 1442 year: 2005 ident: 10.1016/j.bbapap.2016.02.019_bb0400 article-title: Comprehensive label-free method for the relative quantification of proteins from biological samples publication-title: J. Proteome Res. doi: 10.1021/pr050109b contributor: fullname: Higgs – volume: 13 start-page: 666 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0475 article-title: Statistical approach to protein quantification publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M112.025445 contributor: fullname: Gerster – volume: 113 start-page: 2343 year: 2013 ident: 10.1016/j.bbapap.2016.02.019_bb0010 article-title: Protein analysis by shotgun/bottom-up proteomics publication-title: Chem. Rev. doi: 10.1021/cr3003533 contributor: fullname: Zhang – volume: 81 start-page: 6317 year: 2009 ident: 10.1016/j.bbapap.2016.02.019_bb0160 article-title: Effect of dynamic exclusion duration on spectral count based quantitative proteomics publication-title: Anal. Chem. doi: 10.1021/ac9004887 contributor: fullname: Ying Zhang – volume: 57 start-page: 289 year: 1995 ident: 10.1016/j.bbapap.2016.02.019_bb0345 article-title: Controlling the false discovery rate: a practical and powerful approach to multiple testing publication-title: J. R. Stat. Soc. Ser. B Methodol. contributor: fullname: Benjamini – volume: 9 start-page: 2704 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0500 article-title: Increased power for the analysis of label-free LC–MS/MS proteomics data by combining spectral counts and peptide peak attributes publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M110.002774 contributor: fullname: Dicker – volume: 12 start-page: 1996 year: 2013 ident: 10.1016/j.bbapap.2016.02.019_bb0535 article-title: Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current publication-title: J. Proteome Res. doi: 10.1021/pr400100k contributor: fullname: Freund – volume: 82 start-page: 2272 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0205 article-title: Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins publication-title: Anal. Chem. doi: 10.1021/ac9023999 contributor: fullname: Zhang – volume: 13 start-page: 2567 year: 2013 ident: 10.1016/j.bbapap.2016.02.019_bb0505 article-title: Critical assessment of proteome-wide label-free absolute abundance estimation strategies publication-title: Proteomics doi: 10.1002/pmic.201300135 contributor: fullname: Ahrné – volume: 26 start-page: 1574 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0365 article-title: PepC: proteomics software for identifying differentially expressed proteins based on spectral counting publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq171 contributor: fullname: Heinecke – volume: 8 start-page: 5275 year: 2009 ident: 10.1016/j.bbapap.2016.02.019_bb0460 article-title: Protein quantification in label-free LC–MS experiments publication-title: J. Proteome Res. doi: 10.1021/pr900610q contributor: fullname: Clough – year: 1995 ident: 10.1016/j.bbapap.2016.02.019_bb0275 contributor: fullname: Sokal – volume: 12 start-page: 549 year: 2013 ident: 10.1016/j.bbapap.2016.02.019_bb0105 article-title: Tools for label-free peptide quantification publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.R112.025163 contributor: fullname: Nahnsen – volume: 5 start-page: 2339 year: 2006 ident: 10.1016/j.bbapap.2016.02.019_bb0170 article-title: Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae publication-title: J. Proteome Res. doi: 10.1021/pr060161n contributor: fullname: Zybailov – start-page: 163 year: 2003 ident: 10.1016/j.bbapap.2016.02.019_bb0325 article-title: An S-PLUS library for the analysis of differential expression contributor: fullname: Lee – volume: 24 start-page: 7249 year: 2004 ident: 10.1016/j.bbapap.2016.02.019_bb0175 article-title: Cluster analysis of mass spectrometry data reveals a novel component of SAGA publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.24.16.7249-7259.2004 contributor: fullname: Powell – volume: 11 start-page: 2261 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0420 article-title: Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-seq gene expression data publication-title: J. Proteome Res. doi: 10.1021/pr201052x contributor: fullname: Ning – volume: 139 start-page: 138 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0250 article-title: Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current publication-title: Analyst doi: 10.1039/C3AN01738A contributor: fullname: Wu – volume: 9 start-page: 316 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0310 article-title: PatternLab for proteomics: a tool for differential shotgun proteomics publication-title: BMC Bioinf. doi: 10.1186/1471-2105-9-316 contributor: fullname: Carvalho – volume: 5 start-page: 423 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0455 article-title: Reproducibility-optimized test statistic for ranking genes in microarray studies publication-title: IEEE/ACM Trans. Comput. Biol. Bioinform. doi: 10.1109/tcbb.2007.1078 contributor: fullname: Elo – volume: 28 start-page: 83 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0230 article-title: Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1592 contributor: fullname: Griffin – volume: 25 start-page: 2028 year: 2009 ident: 10.1016/j.bbapap.2016.02.019_bb0385 article-title: A statistical framework for protein quantitation in bottom-up MS-based proteomics publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp362 contributor: fullname: Karpievitch – volume: 5 start-page: 1927 year: 2006 ident: 10.1016/j.bbapap.2016.02.019_bb0410 article-title: PEPPeR, a platform for experimental proteomic pattern recognition publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M600222-MCP200 contributor: fullname: Jaffe – volume: 28 start-page: 2404 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0480 article-title: DanteR: an extensible R-based tool for quantitative analysis of -omics data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts449 contributor: fullname: Tom Taverner – volume: 24 start-page: 1556 year: 2008 ident: 10.1016/j.bbapap.2016.02.019_bb0415 article-title: DAnTE: a statistical tool for quantitative analysis of -omics data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn217 contributor: fullname: Polpitiya – volume: 98 start-page: 5116 year: 2001 ident: 10.1016/j.bbapap.2016.02.019_bb0335 article-title: Significance analysis of microarrays applied to the ionizing radiation response publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.091062498 contributor: fullname: Tusher – volume: 137 start-page: 3146 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0245 article-title: NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification publication-title: Analyst doi: 10.1039/c2an35173k contributor: fullname: Wu – volume: 14 start-page: 1993 year: 2015 ident: 10.1016/j.bbapap.2016.02.019_bb0390 article-title: Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics publication-title: J. Proteome Res. doi: 10.1021/pr501138h contributor: fullname: Webb-Robertson – volume: 1 start-page: 317 year: 2002 ident: 10.1016/j.bbapap.2016.02.019_bb0070 article-title: Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry publication-title: J. Proteome Res. doi: 10.1021/pr025517j contributor: fullname: Chelius – volume: 20 start-page: 3551 year: 1999 ident: 10.1016/j.bbapap.2016.02.019_bb0045 article-title: Probability-based protein identification by searching sequence databases using mass spectrometry data publication-title: Eletrophoresis doi: 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 contributor: fullname: Perkins – volume: 26 start-page: 576 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0125 article-title: emPAI Calc—for the estimation of protein abundance from large-scale identification data by liquid chromatography–tandem mass spectrometry publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp700 contributor: fullname: Shinoda – volume: 13 start-page: 493 year: 2013 ident: 10.1016/j.bbapap.2016.02.019_bb0110 article-title: A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC–MS proteomics experiments publication-title: Proteomics doi: 10.1002/pmic.201200269 contributor: fullname: Matzke – volume: 5 start-page: 2909 year: 2006 ident: 10.1016/j.bbapap.2016.02.019_bb0280 article-title: Detecting differential and correlated protein expression in label-free shotgun proteomics publication-title: J. Proteome Res. doi: 10.1021/pr0600273 contributor: fullname: Zhang – volume: 47 start-page: 583 year: 1952 ident: 10.1016/j.bbapap.2016.02.019_bb0290 article-title: Use of ranks in one-criterion variance analysis publication-title: J. Am. Stat. Assoc. doi: 10.1080/01621459.1952.10483441 contributor: fullname: Kruskal – volume: 1 start-page: 161 year: 2002 ident: 10.1016/j.bbapap.2016.02.019_bb0150 article-title: Biomarker discovery in urine by proteomics publication-title: J. Proteome Res. doi: 10.1021/pr015518w contributor: fullname: Pang – volume: 75 start-page: 5437 year: 2012 ident: 10.1016/j.bbapap.2016.02.019_bb0550 article-title: Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli publication-title: J. Proteomics doi: 10.1016/j.jprot.2012.06.020 contributor: fullname: Arike – volume: 13 start-page: 1034 year: 2014 ident: 10.1016/j.bbapap.2016.02.019_bb0520 article-title: Accurate label-free protein quantitation with high- and low-resolution mass spectrometers publication-title: J. Proteome Res. doi: 10.1021/pr401017h contributor: fullname: Krey – volume: 73 start-page: 1740 year: 2010 ident: 10.1016/j.bbapap.2016.02.019_bb0510 article-title: Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods publication-title: J. Proteomics doi: 10.1016/j.jprot.2010.05.011 contributor: fullname: Grossmann |
| SSID | ssj0020775 ssj0025309 |
| Score | 2.4616091 |
| SecondaryResourceType | review_article |
| Snippet | How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen... |
| SourceID | hal proquest crossref pubmed elsevier |
| SourceType | Open Access Repository Aggregation Database Index Database Publisher |
| StartPage | 883 |
| SubjectTerms | Crops, Agricultural - chemistry Crops, Agricultural - metabolism Data processing Life Sciences Mass spectrometry Mass Spectrometry - methods Peptide Peptides - chemistry Peptides - metabolism Plant Proteins - analysis Plant Proteins - metabolism Proteomics - methods Statistics |
| Title | Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics |
| URI | https://dx.doi.org/10.1016/j.bbapap.2016.02.019 https://www.ncbi.nlm.nih.gov/pubmed/26947242 https://search.proquest.com/docview/1796685325 https://search.proquest.com/docview/1808630215 https://hal.science/hal-01532597 |
| Volume | 1864 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9NAEB6VcqCXClIe4VEtCHFbYq_t3eQYRVSBlAqVVvS2mrV31SBw0jYB5cJvZ2ZtR0LiIXGILDtrreOZzHxjf_MtwEutsMKiCnLkq5HMjSnoP4epVCrJK0SnU80Nzu9P9PQ8f3dRXOzApOuFYVplG_ubmB6jdXtk0N7NwXI-H3xMC0P4mxtHM3JNxXE4p2REPv36x5bmoVjiLWqmmkTy6K59LnK8nKOMxKqVqY7Knay38_v0dOuSeZJ_AqExGR3dhf0WRYpxc6H3YMfXPTgY11RBf92IVyLyOuMD8x7cmXRruvVgj7FlI818AOXZ5YI5OZXgz6L24jtubsRqIa7WyByiTfyiZamLqOgwrwU6bh5h9rWgPXIi_0WGa-8FL0pGEXe9bIZyu_PNfTg_enM2mcp2zQVZUqm0knlhRqlDKruo1NCU4TJH-av0BrOg3DCgpxCQIAYdQhFYvWzkMgq2JRJOQcJSD2C3pit-BMKVqUlDmSs6Jw95MkQ0qIynWr7ETCd9kN2ttstGWsN2nLPPtjGNZdPYRFkyTR9MZw_7i4tYiv7_OPMFmW87CStqT8fHlo8RGsqoAjTf0j4876xrySr83gRrT3awFLO0HvK4v4wZUm2YMYDqw8PGNbbzcbOwISj0-L9_wBPY472GePgUdlfXa_-MwNDKHUZvP4Tb48np8Qfevp1NT3g7O_00-wlzSwta |
| link.rule.ids | 230,315,786,790,891,4521,24144,27957,27958,45620,45714 |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9swDCa69NBehi3dI91LG4bdjFh-SMkxCFa4a5rLUqA3gbIlNMPmZG3SIf9-pGwHGLAHsIMPsSXYEWnyY_LxE8B7lWCFeeWjsavGUaZ1Tu8cyihJ4qxCtEoqbnC-nKviKvt0nV8fwLTrhWFaZRv7m5geonV7Ztiu5nC9XA4_y1wT_ubG0ZRcM6E4fJjlWmY9OJycXxTzfd3FKm9BNlXHEU_oOugCzctaSkosXClVEO9kyZ3fZ6gHN0yV_BMODfno7BE8bIGkmDTP-hgOXN2Hk0lNRfS3nfggArUz_Gbeh6Npt61bH44ZXjbqzCdQLm5WTMupBB-r2okfuLsTm5X4vkWmEe3ChZaoLoKow7IWaLl_hAnYgj6RH7mvkb91TvC-ZBR0t-tmKHc83z2Bq7OPi2kRtdsuRCVVS5uIFnEsLVLlRdWGoiSXWkphpdOY-sSOPDqKAjGiV97nngXMxjaleFsiQRUkOPUUejU98XMQtpRa-jJLaE7ms3iEqDHRjsr5ElMVDyDqltqsG3UN09HOvpjGNIZNY-LEkGkGoDt7mF-8xFAC-MfMd2S-_U1YVLuYzAyfI0CUUhGo7-UA3nbWNWQV_usEa0d2MBS2lBrxuL-MGVF5mDKGGsCzxjX29-N-YU1o6PS_v8AbOCoWlzMzO59fvIBjvtLwEF9Cb3O7da8IG23s69b3fwLvOQrY |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Thousand+and+one+ways+to+quantify+and+compare+protein+abundances+in+label-free+bottom-up+proteomics&rft.jtitle=Biochimica+et+biophysica+acta&rft.au=Blein-Nicolas%2C+M%C3%A9lisande&rft.au=Zivy%2C+Michel&rft.date=2016-08-01&rft.issn=0006-3002&rft.volume=1864&rft.issue=8&rft.spage=883&rft.epage=895&rft_id=info:doi/10.1016%2Fj.bbapap.2016.02.019&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1570-9639&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1570-9639&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1570-9639&client=summon |