Dear Skyline Team,

In my phosphoproteomic PRM analysis, I used Proteome Discoverer for database searching and then imported the exported .MSF or .pdResult files into Skyline to build the spectral library. While the library was successfully created, I encountered an issue where many spectra that matched my target peptides were associated with multiple ambiguous peptide-spectrum matches (PSMs). These ambiguous matches were automatically filtered out, resulting in the loss of numerous peptides I need to target. Consequently, after importing my peptide list, many of them failed to match any spectra in the library. What should I do to resolve this?

As follows：
Skyline
Library successfully created. Spectra matching the following peptides previously had multiple ambiguous peptide matches and have been excluded:
AG[+79.96633]Saktalcavem[+15.99492]K
AG[+79.96633]Saktalkewmk
AGS[+79.96633]Vichtalcavem[+15.99492]Q
AGS[+79.96633]Wicktalcavem
Awkwatkandith[+79.96633]Tibbink
Avkoutkandit[+79.96633]Pink
Athaslattuvat[+79.96633]Spask
Adaslatvats[+79.96633]Basque
Ests[+79.96633]Spager
STX[+79.96633]Bakr
Akakkas[+79.96633]Kibaktubsappar
Akkak[+79.96633]Bishop
Akkax[+79.96633]Abcaper
Alex[+79.96633]sk
Alex[+79.96633]sk
Anisnikins[+79.96633]SPKPSK
Anisnigans[+79.96633]Pickups
The [+79.96633]Substituteist
ATS[+79.96633]BSTListxR
Awaaz[+79.96633]Spanchevk
Awas[+79.96633]Pansevak
Aws[+79.96633]Jindpivigiri
Avsnt[+79.96633]BIVKIBIR
Taktak[+79.96633]Hold on
DocTaxSPVT[+79.96633]Q
Delpt[+79.96633]DBsec
Tailft[+79.96633]Bisec
TikBekect[+79.96633]Setlock
TGBEKects[+79.96633]Edluck
DS[+79.96633]Gisvicker
DSS[+79.96633]iCaser
Ectex[+79.96633]Tcivic
Iktekpst[+79.96633]Chekvik
Ideas[+79.96633]sk
Ideas[+79.96633]KK
Itate[+79.96633]Wirpsup
Edaturbs[+79.96633]Bactic
ESP[+79.96633]DSlog
Eggpst[+79.96633]DSlock
EPS[+79.96633]AbsipaikspakupatBabbar
EfSubsipay[+79.96633]GSBayAbir
Afsopsipyks[+79.96633]Spakapir
ESAP[+57.02146]KKS[+79.96633]StandFinder
ESSP[+57.02146]GCS[+79.96633]TPint
ESSp[+57.02146]GCEST[+79.96633]PIN
Estes[+79.96633]
Estes[+79.96633]PK
Faket[+79.96633]Chevpinet
FGETS[+79.96633]Wifnettler
G[+79.96633]Saktalcavem[+15.99492]K
G[+79.96633]Chaktalkevm
KISS[+79.96633]Vichtalkevm[+15.99492]Q
KISS[+79.96633]Wicktalkevm
STST[+79.96633]Swift
Husts[+79.96633]Swithak
Hachtswd[+79.96633]Attic
HTCit[+79.96633]As
Hdisted[+79.96633]Oct
Eas[+79.96633]SVTPIK
IEASS[+79.96633]VTPIK
IEASSVT[+79.96633]PIK
IEDVGS[+79.96633]DEEDDSGK
IEDVGSDEEDDS[+79.96633]GK
IM[+15.99492]PDS[+79.96633]NDSPPAER
IM[+15.99492]PDS[+79.96633]NDSPPAEREPGEVVDSLVGK
IM[+15.99492]PDSNDS[+79.96633]PPAER
IM[+15.99492]PDSNDS[+79.96633]PPAEREPGEVVDSLVGK
ISPS[+79.96633]TDSLAK
ISPST[+79.96633]DSLAK
ISPSTDS[+79.96633]LAK
IT[+79.96633]SPLM[+15.99492]EPSSIEK
ITS[+79.96633]PLM[+15.99492]EPSSIEK
KMT[+79.96633]SPENDSK
KMTS[+79.96633]PENDSK
KPT[+79.96633]ETPPVK
KPTET[+79.96633]PPVK
LDNVSHT[+79.96633]PSSYIETLPK
LDNVSHTPS[+79.96633]SYIETLPK
LDS[+79.96633]TAGM[+15.99492]PNSK
LDST[+79.96633]AGM[+15.99492]PNSK
LIS[+79.96633]SENFENYVR
LISS[+79.96633]ENFENYVR
LLLDPS[+79.96633]STPTK
LLLDPSS[+79.96633]TPTK
LLLDPSST[+79.96633]PTK
LLLDPSSTPT[+79.96633]K
LS[+79.96633]SLVIQM[+15.99492]AR
LS[+79.96633]SLVIQMAR
LSS[+79.96633]LVIQM[+15.99492]AR
LSS[+79.96633]LVIQMAR
LTGQENIS[+79.96633]SK
LTGQENISS[+79.96633]K
M[+15.99492]T[+79.96633]SPENDSK
M[+15.99492]TS[+79.96633]PENDSK
M[+42.01056]ASGNDS[+79.96633]TTVK
M[+42.01056]ASGNDST[+79.96633]TVK
MT[+79.96633]SPENDSK
MTS[+79.96633]PENDSK
NQQEHGGEDS[+79.96633]SQESK
NQQEHGGEDSS[+79.96633]QESK
NSLS[+79.96633]DSADPFLIK
NSLSDS[+79.96633]ADPFLIK
QSPLVTPGS[+79.96633]TTK
QSPLVTPGST[+79.96633]TK
S[+79.96633]ATPPPAEPASLPQEPPK
S[+79.96633]ATVSPQQPQAQQR
S[+79.96633]AVSKIASEMAHEAVELTSSEM[+15.99492]R
S[+79.96633]AVSKIASEMAHEAVELTSSEMR
S[+79.96633]ESTM[+15.99492]SPSENVSR
S[+79.96633]PSALLDYYQEDVSRPQPETQESSGR
S[+79.96633]SGTAPAPASPSPPEPGPGGEAESVR
S[+79.96633]SSPVGLAK
S[+79.96633]STHGEGAAEADDK
S[+79.96633]STSQGSGSTPVPEALR
S[+79.96633]TPGPQLPTR
SAT[+79.96633]PPPAEPASLPQEPPK
SATVS[+79.96633]PQQPQAQQR
SAVS[+79.96633]KIASEMAHEAVELTSSEM[+15.99492]R
SAVS[+79.96633]KIASEMAHEAVELTSSEMR
SES[+79.96633]TM[+15.99492]SPSENVSR
SES[+79.96633]TMSPSENVSR
SEST[+79.96633]M[+15.99492]SPSENVSR
SEST[+79.96633]MSPSENVSR
SESTM[+15.99492]S[+79.96633]PSENVSR
SESTM[+15.99492]SPS[+79.96633]ENVSR
SESTM[+15.99492]SPSENVS[+79.96633]R
SESTMS[+79.96633]PSENVSR
SESTMSPS[+79.96633]ENVSR
SPS[+79.96633]ALLDYYQEDVSRPQPETQESSGR
SQS[+79.96633]AAVTPSSSTSSAR
SQSAAVT[+79.96633]PSSSTSSAR
SS[+79.96633]GTAPAPASPSPPEPGPGGEAESVR
SS[+79.96633]SPVGLAK
SS[+79.96633]THGEGAAEADDK
SS[+79.96633]TSQGSGSTPVPEALR
SSNTDSSSSS[+79.96633]SPGNIK
SSNTDSSSSSS[+79.96633]PGNIK
SSS[+79.96633]PVGLAK
SST[+79.96633]HGEGAAEADDK
SSTSQGS[+79.96633]GSTPVPEALR
SSTSQGSGST[+79.96633]PVPEALR
ST[+79.96633]GPTLSSPR
ST[+79.96633]PGPQLPTR
STGPT[+79.96633]LSSPR
STGPTLS[+79.96633]SPR
STGPTLSS[+79.96633]PR
SVS[+79.96633]TPSEAGSQDSGDGAVGSR
SVSSNVAS[+79.96633]VSPIPAGSK
SVSSNVASVS[+79.96633]PIPAGSK
SVST[+79.96633]PSEAGSQDSGDGAVGSR
T[+79.96633]FSLSAR
T[+79.96633]GATASPSAEALPPK
T[+79.96633]GSESSQTGASATSGR
T[+79.96633]GSISSQSNSGPR
TFS[+79.96633]LSAR
TGAT[+79.96633]ASPSAEALPPK
TGATAS[+79.96633]PSAEALPPK
TGATASPS[+79.96633]AEALPPK
TGS[+79.96633]ESSQTGASATSGR
TGS[+79.96633]ISSQSNSGPR
TGSES[+79.96633]SQTGASATSGR
TGSESS[+79.96633]QTGASATSGR
TPSGGVFFES[+79.96633]SVTR
TPSGGVFFESS[+79.96633]VTR
TPSGGVFFESSVT[+79.96633]R
TPVQSQQPSAT[+79.96633]TPSGADEK
TPVQSQQPSATT[+79.96633]PSGADEK
TVGTPIASVPGS[+79.96633]TNTGTVPGSEK
TVGTPIASVPGST[+79.96633]NTGTVPGSEK
VPVAPS[+79.96633]STTR
VPVAPSS[+79.96633]TTR
VPVAPSST[+79.96633]TR
VPVAPSSTT[+79.96633]R
Y[+79.96633]TLTPGSGYLIR
YSNNGAALAELEEQAALVGS[+79.96633]GSR
YSNNGAALAELEEQAALVGSGS[+79.96633]R
YT[+79.96633]LTPGSGYLIR
YTLT[+79.96633]PGSGYLIR
Confirm