I. SEARCH PARAMETERS AND ACCEPTANCE CRITERIA

Transcription

1 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry The identificatin f prteins r peptides is cmmnly accmplished by peptide sequencing (MS/MS analyses), peptide mass fingerprinting (PMF), r sme cmbinatin f bth. Bth methds typically depend n acquiring mass spectra, cnversin f data int a frmat fr searching, fllwed by interpretatin via matching the data against a sequence database r spectral library with an apprpriate search engine. Many parameters are cmmn t the tw appraches and sme are unique t each. Similarly, pst translatinal mdificatins (PTMs) can affect prtein identificatins; their determinatin/lcalizatin may als be the bjective f the experiment. In additin, quantificatin by istpe dependent r istpe free methds may be an additinal aspect f the data set. The fllwing guidelines describe the infrmatin required by the jurnal fr articles dealing with mass spectrmetric analyses designed fr prtein, peptide r PTM identificatin and their quantificatin. Manuscripts that use generated datasets fr sftware r algrithm develpment may prvide nly the parameters in sectin I belw prviding they d NOT reprt the identities f the peptides r prteins used. If identificatins r sequences are listed, the requirements f Sectin II (and III, if germane) must be met. I. SEARCH PARAMETERS AND ACCEPTANCE CRITERIA The fllwing supprting infrmatin shuld be included in the Experimental sectin f the manuscript fr either MS/MS r PMF analyses (recgnizing that sme sftware d nt explicitly prvide sme f these parameters): Peak Lists: The methd and/r prgram (including versin number and/r date) used t create the "peak lists" frm the riginal data and the parameters used in the creatin f this peak list, particularly any prcessing which might affect the quality f the subsequent database search. Examples include smthing, any signal t nise threshlding, charge states assignment r de istping, etc. In cases where additinal custmized prcessing f the cllectins f peak lists has been perfrmed, e.g. clustering r filtering, the methd and/r prgram (including versin number) shuld be referenced. Search Engine: The name and versin (r release date) f all prgrams used fr database searching must be prvided. Sequence Database r Spectral Library: The name and versin (r release date) f all sequence database(s) r spectral libraries used must be listed. If a database r library was cmpiled in huse, a cmplete descriptin f the surce f the Page 1 f 7

2 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry sequences r spectra is required and the sftware used fr library generatin. The number f entries actually searched frm each database r library shuld be included. If the database r library used is very small (<1000 entries) r excludes cmmn cntaminants, justificatin must be specifically prvided since this may generate misleading assignments and an inaccurate false discvery rate estimate. Enzyme specificity: A descriptin f all enzymes used t generate peptides, including the number f missed and nn specific cleavages (e.g. semi tryptic) permitted, must be listed. Fixed mdificatin(s); A list f all mdificatins cnsidered (including residue specificity) must be given. Variable mdificatins: A list f all mdificatins cnsidered (including residue specificity) must be given. Mass tlerance fr precursr ins. Mass tlerance fr fragment ins (nt required fr PMF data). Knwn cntaminants excluded (particularly fr PMF data): All mitted peaks frm pre designated cntaminants (r if any f these fragments are used fr calibratin) must be identified. Threshld scre/expectatin value: Criteria used fr accepting individual spectra shuld be stated alng with a justificatin. False Discvery Rates at Peptide and Prtein levels: Fr large scale experiments, the results f any additinal statistical analyses that estimate a measure f identificatin certainty fr the dataset, r allw a determinatin f the false discvery rate, e.g., the results f decy searches r ther cmputatinal appraches. II. PROTEIN AND PEPTIDE IDENTIFICATION The infrmatin belw fr each prtein and peptide sequence identified shuld be specified in the Results (r Supplemental) sectin. If the identificatins are presented nly at the peptide level, then prtein level infrmatin may be mitted. All peptide sequences assigned: A list (in ne r mre Tables), nting any deviatin frm the expected enzyme cleavage specificity, must be prvided. Precursr charge and mass/charge: These parameters shuld be listed fr each peptide assignment in the same table. All mdificatins bserved. Page 2 f 7

3 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry Number f matched and unmatched masses: Fr PMF data, the ttal number f peaks, bth matched and unmatched, shuld be listed in the identificatin table. Scre(s): The relevant scre (depending n the sftware used) and any assciated statistical infrmatin btained fr searches cnducted must be prvided fr each peptide. Prtein accessin number and sequence database r spectral library surce. Cunt f the number f distinct peptide sequences assigned t each prtein: When cmputing this number, multiple matches t peptides with the same primary sequence shuld be cunted as a single distinct peptide, including multiple matches that represent different precursr charge states r mdificatin states. Any alternative assumptins must be justified. Prtein sequence % cverage: This value shuld be expressed as the number f amin acids spanned by the assigned peptides divided by the sequence length X 100. Alternatively, a derived prtein identificatin prbability can be given. Fr all prteins identified n the basis f ne unique peptide spectrum, (a peptide mass fingerprint spectrum cunts as ne spectrum), the ability t view anntated spectra fr these identificatins must be made available. This can be achieved in ne f three ways: Submissin f all spectra and search results t a public results repsitry that is equipped with a spectral viewer prir t submissin f the manuscript t the jurnal. This infrmatin will appear as a hyperlink in the published article. Submissin (with the manuscript) f spectra and search results in a file frmat that allws visualizatin f the spectra using a freely available viewer. Submissin (with the manuscript) f anntated spectra in an ffice r PDF frmat. Nte: Files submitted thrugh the nline manuscript submissin prcess must be less than 100 MB in size. If files are greater than 100 MB in size, the jurnal recmmends depsiting the file in a suitable repsitry, such as Tranche [ then supplying the hash frm Tranche (r ther identificatin cde if a different repsitry is used) in the manuscript and in the cver letter accmpanying the manuscript submissin. Psting f results n the authr s website as the sle surce f this data des nt satisfy this requirement, as the ability t annymusly access the data is necessary fr the review prcess. Page 3 f 7

4 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry III. POST TRANSLATIONAL MODIFICATIONS Studies fcusing n psttranslatinal mdificatins (PTMs) require specialized methdlgy and dcumentatin t assign the type(s) and site(s) f the mdificatin(s). The guidelines in this sectin apply t PTMs that ccur under physilgical cnditins and t which bilgical significance may be assigned, such as phsphrylatin, glycsylatin, etc. as well as purpsefully induced chemical mdificatins f central imprtance t the results f the study, such as chemical crss linking. These guidelines d nt apply t cmmn mdificatins arising frm sample handling r preparatin such as xidatin f Met r alkylatin f Cys. In additin t the tabular presentatin(s) f the data described in guideline II, the fllwing infrmatin is required: The site(s) f mdificatin: Within each peptide sequence, all mdificatins must be clearly lcated (unless ambiguus; see belw) and the manner in which this was accmplished (thrugh cmputatin r manual inspectin) must be described. A justificatin fr any lcalizatin scre threshld emplyed. Ambiguus assignments: Peptides cntaining ambiguus PTM site lcalizatins must be listed in a separate table frm thse with unambiguus site lcalizatins. In cases where there are multiple mdificatin sites and at least ne is ambiguus, then these peptides shuld be listed with the ambiguus assignments. Ambiguus assignments must be clearly labeled as such. Examples f ambiguities include: Mdified peptides in which ne r mre mdificatin sites are ambiguus. Instances where the peptide sequence is repeated in the same prtein s the specific mdificatin site cannt be assigned. Instances in which the same peptide is repeated in multiple prteins, e.g. splice variants and paralgs (See als Sectin IV). Isbaric mdificatins (e.g., acetylatin vs. trimethylatin, phsphrylatin vs. sulfnatin etc), where the pssibilities may nt be distinguished. Examples f methds able t distinguish between these include mass spectrmetric appraches such as accurate mass determinatin, bservatin f signature fragment ins (e.g. m/z 79 vs. m/z 80 in negative in mde fr assignment f phsphrylatin ver sulfnatin), r bilgical r chemical strategies. Page 4 f 7

5 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry Anntated, mass labeled spectra: Spectra fr all mdified peptides must be either submitted t a public repsitry r accmpany the manuscript as described in guideline II. IV. PROTEIN INFERENCE FROM PEPTIDE ASSIGNMENTS Since prtein identificatin experiments that are based n prtelytic digestin and subsequent characterizatin f the resulting peptides result in the lss f cnnectivity between these peptides and their prtein precursrs, identificatins based n the assignment f peptide sequences can result in a cmbinatin f tw pssible utcmes: distinct peptides that map t nly ne prtein sequence r peptides that are cmmn t mre than ne prtein sequence (prtein grup) arising, fr example, frm alternative splicing. When identificatins are f the latter type, authrs are required (in additin t the tabular presentatin(s) f the data described in guideline II) t: Prvide accessin numbers (r ther identifiers) fr all prteins that were cmbined int the grup. Authrs shuld justify any cases where a single prtein frm a prtein grup has been singled ut r when asserting that mre than ne indistinguishable member f a prtein grup is actually present. Prvide a summary list f cmmn peptides belnging t each prtein grup and thse distinct t a specific prtein. State (and justify) if prteins are identified frm a different species than the ne being studied. Fr example, identificatin f a muse r human prtein in a hamster study. V. QUANTIFICATION Manuscripts presenting quantitative prtemic results must prvide the fllwing infrmatin: All relevant quantificatin data (as part f the peptide and prtein identificatin tables), alng with a descriptin f hw the raw data were prcessed t prduce these measurements. A descriptin f hw the analytical reliability f measurements was validated using technical replicates and statistical methds. Citatin f standard methds r specialized sftware may be used. Hwever, it is essential t demnstrate that the data cntained in the manuscript actually cnfrm t the same mdels. Page 5 f 7

6 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry A descriptin f hw the bilgical reliability f measurements was validated using bilgical replicates, statistical methds, independent experiments, etc. Studies based n a single bilgical experiment are generally nt acceptable (except as a dataset t test biinfrmatic systems). If a bilgical replicate frm the same surce cannt be perfrmed (e.g. patient sample), a large enugh number f similar bilgical samples, apprpriately justified, must be perfrmed in rder t enable sund cnclusins. A descriptin f the treatment f relevant systematic errr effects such as interference frm verlapping precursr ins, incmplete istpe labeling, bias crrectin fr pipetting errr, etc. A descriptin f the treatment f randm errr issues such as utlier rejectin and the categrical exclusin f data by threshlds; fr example, based n signal t nise r minimum in cunts. Prper estimates f uncertainty and the methds used fr the errr analysis. Quantificatin f many prteins r peptides generally results in the need t use sme frm f multiple hypthesis testing crrectin. Whenever pssible, cnfidence in prtein quantificatin shuld be prvided fr each individual prtein rather than the glbal dataset. Any cnclusins drawn r hypthesis generated frm the quantitative data in the manuscript must be in cncert with the determined estimate f uncertainty. If a cmpnent is nt being identified by database searching in a particular experiment, assurance f the identity f the analyte being measured and the specificity (e.g. presence/absence f interference) with which it is measured must be prvided. This particularly applies t intensity based methds such as SELDI, selected reactin mnitring / multiple reactin mnitring (SRM/MRM) and accurate mass and retentin time (AMT) based methds. A descriptin f the way multiple isfrms in a prtein grup were quantified. Fr spectral cunting measurements, in additin t the abve guidelines, additinal details shuld be prvided such as whether numbers f peptides r spectra were cunted, whether mdified peptides, semi tryptic peptides r shared peptides were cunted, and whether r nt dynamic exclusin was used, etc. VI. RAW DATA SUBMISSION Page 6 f 7

7 Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry If a manuscript is accepted by the jurnal, all mass spectra cntributing t the described wrk must be depsited in electrnic frm by the time f publicatin at a publicly accessible site that is independent f the authrs' cntrl. Submissin f all mass spectrmetric utput files in the riginal instrument vendr file frmat is the preferred and mst direct means f meeting this requirement. Data cnversin t an pen frmat such as mzml is encuraged if sftware capable f reading the instrument vendr file frmat is nt widely available. In all cases, the spectra are expected t be prvided in a frm prir t any prcessing that might affect the quality f subsequent interpretatin as described in the peak list guideline (See sectin I). The editrs f MCP recgnize that uplading large datasets can smetimes engender unfreseen difficulties and authrs encuntering prblems shuld cntact the Bethesda ffice fr advice and/r assistance. Authrs will nt be penalized fr delays resulting frm such difficulties. Requests fr exemptins (r delays nt related t technical prblems) frm this requirement must be made in writing t ne f the c editrs at the time f submissin. Upn acceptance f the manuscript (and by the time f publicatin), authrs shuld prvide a URL and passwrd, if apprpriate, fr accessing the data. This will be listed as part f the published article. e.g. The data assciated with this manuscript may be dwnladed frm PrtemeCmmns.rg Tranche, using the fllwing hash: JyU4hPRjRHPMtNMpO1DziH5R5KzLAXJ8MDwDe4mqL07AslL5imsCyjcYwt2eSZKTEpiKF7 qbc+ldijersjfeddz5fiaaaaaaaab0g== Further infrmatin regarding this requirement can be btained by cntacting mcpnline@asbmb.rg. Page 7 f 7