Database search has become one of the most important method to interpret LC-MS/MS data in proteomics, Many algorithms to identify peptides in MS/MS data have been proposed, Including Mascot, Sequest, X!Tandem, ProVerB and SQID. However, many of them mainly based on peak matches or peak intensity, not on peak intensity identifiability. On the basis of this matter, this article provides a new perspective and characteristics reference information, scilicet PROPIN, which is a novel peptide identification algorithm based on peak intensity identifiability. Compared with Mascot, Sequest, PROPIN identified significantly more peptides from LC-MS/MS data sets at 1% False Discovery Rate (FDR), and also showing its robustness and versatility on various platforms and experimental data sets.
REFERENCES
1.
Li
W
, Ji
L
, Goya
J
, Tan
G
, Wysocki
VH
. SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry
. J Proteome Res
10
: 1593
–1602
(2011
).2.
Karas
M
, Hillenkamp
F.
Laser desorption ionization of proteins with molecular masses exceeding 10, 000 daltons
. Analytical chemistry
60
: 2299
–2301
(1988
).3.
Fenn
JB
, Mann
M
, Meng
CK
, Wong
SF
, Whitehouse
CM
. Electrospray ionization for mass spectrometry of large biomolecules
. Science
246
: 64
–71
(1989
).4.
Yadav
AK
, Kumar
D
, and Dash
D.
MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry
. J Proteome Res
10
: 2154
–2160
(2011
).5.
Xiao
C-L
, Chen
X-Z
, Du
Y-L
, Sun
X
, Zhang
G
, et al Binomial Probability Distribution Model-Based Protein Identification Algorithm for Tandem Mass Spectrometry Utilizing Peak Intensity Information
. Journal of Proteome Research
12
: 328
–335
(2012
).6.
Nesvizhskii
AI
, Vitek
O
, Aebersold
R.
Analysis and validation of proteomic data generated by tandem mass spectrometry
. Nature methods
4
: 787
–797
(2007
).7.
Cottrell
J
, London
U.
Probability-based protein identification by searching sequence databases using mass spectrometry data
. Electrophoresis
20
: 3551
–3567
(1999
).8.
Eng
JK
, McCormack
AL
, Yates Iii
JR
. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
. Journal of the American Society for Mass Spectrometry
5
: 976
–989
(1994
).9.
Craig
R
, Beavis
RC
. TANDEM: matching proteins with tandem mass spectra
. Bioinformatics
20
: 1466
–1467
(2004
).10.
An
MR
, Zou
X
, Wang
QS
, Zhao
XY
, Wu
J
, et al High-Confidence de Novo Peptide Sequencing Using Positive Charge Derivatization and Tandem MS Spectra Merging
. Analytical Chemistry
85
: 4530
–4537
(2013
).11.
Cox
J
, Neuhauser
N
, Michalski
A
, Scheltema
RA
, Olsen
JV
, et al Andromeda: a peptide search engine integrated into the MaxQuant environment
. J Proteome Res
10
: 1794
–1805
(2011
).12.
Dagda
RK
, Sultana
T
, Lyons-Weiler
J.
Evaluation of the consensus of four peptide identification algorithms for tandem mass spectrometry based proteomics
. Journal of proteomics & bioinformatics
3
: 39
(2010
).13.
Kapp
EA
, Schütz
F
, Connolly
LM
, Chakel
JA
, Meza
JE
, et al An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis
. Proteomics
5
: 3475
–3490
(2005
).14.
Geer
LY
, Markey
SP
, Kowalak
JA
, Wagner
L
, Xu
M
, et al Open mass spectrometry search algorithm
. Journal of proteome research
3
: 958
–964
(2004
).15.
Xiao
CL
, Chen
XZ
, Du
YL
, Li
ZF
, and Wei
L
, et al Dispec: A Novel Peptide Scoring Algorithm Based on Peptide Matching Discriminability
. Plos One
8
(2013
).16.
Klimek
J
, Eddes
JS
, Hohmann
L
, Jackson
J
, Peterson
A
, et al The standard protein mix database: a diverse data set to assist in the production of improved peptide and protein identification software tools
. The Journal of Proteome Research
7
: 96
–103
(2007
).17.
Fu
Y
, Xiu
L-Y
, Jia
W
, Ye
D
, Sun
R-X
, et al DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data
. Molecular & Cellular Proteomics
10
(2011
).18.
Ramakrishnan
SR
, Vogel
C
, Prince
JT
, Wang
R
, Li
Z
, et al Integrating shotgun proteomics and mRNA expression data to improve protein identification
. Bioinformatics
25
: 1397
–1403
(2009
).19.
Käll
L
, Storey
JD
, MacCoss
MJ
, Noble
WS
. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
. Journal of proteome research
7
: 29
–34
(2007
).20.
Elias
JE
, Haas
W
, Faherty
BK
, Gygi
SP
. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
. Nature methods
2
: 667
–675
(2005
).21.
Goeminne
LJ
, Gevaert
K
, Clement
L.
Experimental design and data-analysis in label-free quantitative LC/MS proteomics: A tutorial with MSqRob
. Journal of Proteomics
; 171
:23
–36
(2017
).22.
Townsend
C
, Furukawa
A
, Schwochert
J
, Pye
C
, Edmondson
Q
, Lokey
RS
. CycLS: Accurate, whole-library sequencing of cyclic peptides using tandem mass spectrometry
. Bioorganic & Medicinal Chemistry.
26
:1232
–1238
(2018
).23.
Kong
AT
, Leprevost
FV
, Avtonomov
DM
, Mellacheruvu
D
, Nesvizhskii
AI
. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
. Nature Methods.
14
:513
–520
(2017
).© 2019 Author(s).
2019
Author(s)
